# Reading DEGs list exp1

# all model including subset data
DEG.objs.e1.v3.0annotation.all<-list.files(path=file.path("..","v3.0annotation","20170617-samples","output","FULLtoptag"),
           pattern="(^leaf|^root)(\\.)(.+)(v3.0anno)(.csv)") 
# read csv file (only full model)
DEG.count.list.e1.v3.0annotation.all<-lapply(DEG.objs.e1.v3.0annotation.all, function(x) read_csv(paste(file.path("..","v3.0annotation","20170617-samples","output","FULLtoptag"),"/",x,sep="")))
names(DEG.count.list.e1.v3.0annotation.all)<-gsub(".csv","",DEG.objs.e1.v3.0annotation.all)
DEG.count.list.e1.v3.0annotation.all[["root.R500.trtlive.DEGs.all.rD.v3.0anno"]] %>% filter(FDR<0.05)
# A tibble: 383 x 11
      X1 genes  logFC logCPM    LR  PValue     FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>   <dbl>   <dbl> <chr> <chr>    
 1     1 BraA…  1.26    4.60  33.9 5.82e-9 1.55e-4 AT1G… NLP4     
 2     2 BraA…  2.13    3.39  32.5 1.20e-8 1.60e-4 AT1G… <NA>     
 3     3 BraA…  2.23    1.67  31.4 2.05e-8 1.83e-4 AT3G… ABCA3    
 4     4 BraA…  1.70    3.81  30.6 3.14e-8 1.93e-4 AT3G… NF-YA6   
 5     5 BraA… -1.53    4.64  30.3 3.61e-8 1.93e-4 AT4G… <NA>     
 6     6 BraA…  1.28    3.98  29.2 6.42e-8 2.86e-4 AT5G… GLN1;4   
 7     7 BraA… -1.14    5.84  28.4 1.00e-7 3.29e-4 AT1G… AtNIGT1  
 8     8 BraA…  0.988   5.18  28.2 1.09e-7 3.29e-4 AT5G… <NA>     
 9     9 BraA…  1.77    5.64  28.2 1.12e-7 3.29e-4 AT5G… ATDUR3   
10    10 BraA… -1.37    3.74  27.9 1.30e-7 3.29e-4 AT1G… AtNIGT1  
# ... with 373 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>
names(DEG.count.list.e1.v3.0annotation.all)
 [1] "leaf.FPsc.trtlive.DEGs.all.rD.v3.0anno"                                                       
 [2] "leaf.genotypeFPsc_trt5E_live.genotypeFPsc_trt5E_dead.genotypeFPsc.DEGs.int.rB.rR500.v3.0anno" 
 [3] "leaf.genotypeFPsc_trt5E_live.genotypeFPsc_trtBLANK_NA.genotypeFPsc.DEGs.int.rD.rR500.v3.0anno"
 [4] "leaf.genotypeFPsc.DEGs.add.rB.rR500.v3.0anno"                                                 
 [5] "leaf.genotypeFPsc.DEGs.add.rD.rR500.v3.0anno"                                                 
 [6] "leaf.genotypeR500_trt5E_live.genotypeR500_trt5E_dead.genotypeR500.DEGs.int.rB.rFPsc.v3.0anno" 
 [7] "leaf.genotypeR500_trt5E_live.genotypeR500_trtBLANK_NA.genotypeR500.DEGs.int.rD.rFPsc.v3.0anno"
 [8] "leaf.genotypeR500.DEGs.add.rB.rFPsc.v3.0anno"                                                 
 [9] "leaf.genotypeR500.DEGs.add.rD.rFPsc.v3.0anno"                                                 
[10] "leaf.R500.trtlive.DEGs.all.rD.v3.0anno"                                                       
[11] "leaf.trt5E_dead.DEGs.add.rB.rFPsc.v3.0anno"                                                   
[12] "leaf.trt5E_dead.DEGs.add.rB.rR500.v3.0anno"                                                   
[13] "leaf.trt5E_dead.genotypeFPsc_trt5E_dead.DEGs.int.rB.rR500.v3.0anno"                           
[14] "leaf.trt5E_dead.genotypeR500_trt5E_dead.DEGs.int.rB.rFPsc.v3.0anno"                           
[15] "leaf.trt5E_live.DEGs.add.rB.rFPsc.v3.0anno"                                                   
[16] "leaf.trt5E_live.DEGs.add.rB.rR500.v3.0anno"                                                   
[17] "leaf.trt5E_live.DEGs.add.rD.rFPsc.v3.0anno"                                                   
[18] "leaf.trt5E_live.DEGs.add.rD.rR500.v3.0anno"                                                   
[19] "leaf.trt5E_live.genotypeFPsc_trt5E_live.DEGs.int.rB.rR500.v3.0anno"                           
[20] "leaf.trt5E_live.genotypeFPsc_trt5E_live.DEGs.int.rD.rR500.v3.0anno"                           
[21] "leaf.trt5E_live.genotypeFPsc.DEGs.int.rB.rR500.v3.0anno"                                      
[22] "leaf.trt5E_live.genotypeFPsc.DEGs.int.rD.rR500.v3.0anno"                                      
[23] "leaf.trt5E_live.genotypeR500_trt5E_live.DEGs.int.rB.rFPsc.v3.0anno"                           
[24] "leaf.trt5E_live.genotypeR500_trt5E_live.DEGs.int.rD.rFPsc.v3.0anno"                           
[25] "leaf.trt5E_live.genotypeR500.DEGs.int.rB.rFPsc.v3.0anno"                                      
[26] "root.FPsc.trtlive.DEGs.all.rD.v3.0anno"                                                       
[27] "root.genotypeFPsc_trt5E_live.genotypeFPsc_trt5E_dead.genotypeFPsc.DEGs.int.rB.rR500.v3.0anno" 
[28] "root.genotypeFPsc_trt5E_live.genotypeFPsc_trtBLANK_NA.genotypeFPsc.DEGs.int.rD.rR500.v3.0anno"
[29] "root.genotypeFPsc.DEGs.add.rB.rR500.v3.0anno"                                                 
[30] "root.genotypeFPsc.DEGs.add.rD.rR500.v3.0anno"                                                 
[31] "root.genotypeR500_trt5E_live.genotypeR500_trt5E_dead.genotypeR500.DEGs.int.rB.rFPsc.v3.0anno" 
[32] "root.genotypeR500_trt5E_live.genotypeR500_trtBLANK_NA.genotypeR500.DEGs.int.rD.rFPsc.v3.0anno"
[33] "root.genotypeR500.DEGs.add.rB.rFPsc.v3.0anno"                                                 
[34] "root.genotypeR500.DEGs.add.rD.rFPsc.v3.0anno"                                                 
[35] "root.R500.trtlive.DEGs.all.rD.v3.0anno"                                                       
[36] "root.trt5E_dead.DEGs.add.rB.rFPsc.v3.0anno"                                                   
[37] "root.trt5E_dead.DEGs.add.rB.rR500.v3.0anno"                                                   
[38] "root.trt5E_dead.genotypeFPsc_trt5E_dead.DEGs.int.rB.rR500.v3.0anno"                           
[39] "root.trt5E_dead.genotypeR500_trt5E_dead.DEGs.int.rB.rFPsc.v3.0anno"                           
[40] "root.trt5E_live.DEGs.add.rB.rFPsc.v3.0anno"                                                   
[41] "root.trt5E_live.DEGs.add.rB.rR500.v3.0anno"                                                   
[42] "root.trt5E_live.DEGs.add.rD.rFPsc.v3.0anno"                                                   
[43] "root.trt5E_live.DEGs.add.rD.rR500.v3.0anno"                                                   
[44] "root.trt5E_live.genotypeFPsc_trt5E_live.DEGs.int.rB.rR500.v3.0anno"                           
[45] "root.trt5E_live.genotypeFPsc_trt5E_live.DEGs.int.rD.rR500.v3.0anno"                           
[46] "root.trt5E_live.genotypeFPsc.DEGs.int.rB.rR500.v3.0anno"                                      
[47] "root.trt5E_live.genotypeFPsc.DEGs.int.rD.rR500.v3.0anno"                                      
[48] "root.trt5E_live.genotypeR500_trt5E_live.DEGs.int.rB.rFPsc.v3.0anno"                           
[49] "root.trt5E_live.genotypeR500_trt5E_live.DEGs.int.rD.rFPsc.v3.0anno"                           
[50] "root.trt5E_live.genotypeR500.DEGs.int.rB.rFPsc.v3.0anno"                                      
# FDR<0.05
DEG.count.list.e1.v3.0annotation.all %>% map(filter(FDR<0.05)) # does not work
Error in filter(FDR < 0.05): object 'FDR' not found
DEG.count.list.e1.v3.0annotation.all.FDR0.05<-DEG.count.list.e1.v3.0annotation.all %>% map(function(df) filter(df,FDR<0.05)) # does work
names(DEG.count.list.e1.v3.0annotation.all.FDR0.05)
 [1] "leaf.FPsc.trtlive.DEGs.all.rD.v3.0anno"                                                       
 [2] "leaf.genotypeFPsc_trt5E_live.genotypeFPsc_trt5E_dead.genotypeFPsc.DEGs.int.rB.rR500.v3.0anno" 
 [3] "leaf.genotypeFPsc_trt5E_live.genotypeFPsc_trtBLANK_NA.genotypeFPsc.DEGs.int.rD.rR500.v3.0anno"
 [4] "leaf.genotypeFPsc.DEGs.add.rB.rR500.v3.0anno"                                                 
 [5] "leaf.genotypeFPsc.DEGs.add.rD.rR500.v3.0anno"                                                 
 [6] "leaf.genotypeR500_trt5E_live.genotypeR500_trt5E_dead.genotypeR500.DEGs.int.rB.rFPsc.v3.0anno" 
 [7] "leaf.genotypeR500_trt5E_live.genotypeR500_trtBLANK_NA.genotypeR500.DEGs.int.rD.rFPsc.v3.0anno"
 [8] "leaf.genotypeR500.DEGs.add.rB.rFPsc.v3.0anno"                                                 
 [9] "leaf.genotypeR500.DEGs.add.rD.rFPsc.v3.0anno"                                                 
[10] "leaf.R500.trtlive.DEGs.all.rD.v3.0anno"                                                       
[11] "leaf.trt5E_dead.DEGs.add.rB.rFPsc.v3.0anno"                                                   
[12] "leaf.trt5E_dead.DEGs.add.rB.rR500.v3.0anno"                                                   
[13] "leaf.trt5E_dead.genotypeFPsc_trt5E_dead.DEGs.int.rB.rR500.v3.0anno"                           
[14] "leaf.trt5E_dead.genotypeR500_trt5E_dead.DEGs.int.rB.rFPsc.v3.0anno"                           
[15] "leaf.trt5E_live.DEGs.add.rB.rFPsc.v3.0anno"                                                   
[16] "leaf.trt5E_live.DEGs.add.rB.rR500.v3.0anno"                                                   
[17] "leaf.trt5E_live.DEGs.add.rD.rFPsc.v3.0anno"                                                   
[18] "leaf.trt5E_live.DEGs.add.rD.rR500.v3.0anno"                                                   
[19] "leaf.trt5E_live.genotypeFPsc_trt5E_live.DEGs.int.rB.rR500.v3.0anno"                           
[20] "leaf.trt5E_live.genotypeFPsc_trt5E_live.DEGs.int.rD.rR500.v3.0anno"                           
[21] "leaf.trt5E_live.genotypeFPsc.DEGs.int.rB.rR500.v3.0anno"                                      
[22] "leaf.trt5E_live.genotypeFPsc.DEGs.int.rD.rR500.v3.0anno"                                      
[23] "leaf.trt5E_live.genotypeR500_trt5E_live.DEGs.int.rB.rFPsc.v3.0anno"                           
[24] "leaf.trt5E_live.genotypeR500_trt5E_live.DEGs.int.rD.rFPsc.v3.0anno"                           
[25] "leaf.trt5E_live.genotypeR500.DEGs.int.rB.rFPsc.v3.0anno"                                      
[26] "root.FPsc.trtlive.DEGs.all.rD.v3.0anno"                                                       
[27] "root.genotypeFPsc_trt5E_live.genotypeFPsc_trt5E_dead.genotypeFPsc.DEGs.int.rB.rR500.v3.0anno" 
[28] "root.genotypeFPsc_trt5E_live.genotypeFPsc_trtBLANK_NA.genotypeFPsc.DEGs.int.rD.rR500.v3.0anno"
[29] "root.genotypeFPsc.DEGs.add.rB.rR500.v3.0anno"                                                 
[30] "root.genotypeFPsc.DEGs.add.rD.rR500.v3.0anno"                                                 
[31] "root.genotypeR500_trt5E_live.genotypeR500_trt5E_dead.genotypeR500.DEGs.int.rB.rFPsc.v3.0anno" 
[32] "root.genotypeR500_trt5E_live.genotypeR500_trtBLANK_NA.genotypeR500.DEGs.int.rD.rFPsc.v3.0anno"
[33] "root.genotypeR500.DEGs.add.rB.rFPsc.v3.0anno"                                                 
[34] "root.genotypeR500.DEGs.add.rD.rFPsc.v3.0anno"                                                 
[35] "root.R500.trtlive.DEGs.all.rD.v3.0anno"                                                       
[36] "root.trt5E_dead.DEGs.add.rB.rFPsc.v3.0anno"                                                   
[37] "root.trt5E_dead.DEGs.add.rB.rR500.v3.0anno"                                                   
[38] "root.trt5E_dead.genotypeFPsc_trt5E_dead.DEGs.int.rB.rR500.v3.0anno"                           
[39] "root.trt5E_dead.genotypeR500_trt5E_dead.DEGs.int.rB.rFPsc.v3.0anno"                           
[40] "root.trt5E_live.DEGs.add.rB.rFPsc.v3.0anno"                                                   
[41] "root.trt5E_live.DEGs.add.rB.rR500.v3.0anno"                                                   
[42] "root.trt5E_live.DEGs.add.rD.rFPsc.v3.0anno"                                                   
[43] "root.trt5E_live.DEGs.add.rD.rR500.v3.0anno"                                                   
[44] "root.trt5E_live.genotypeFPsc_trt5E_live.DEGs.int.rB.rR500.v3.0anno"                           
[45] "root.trt5E_live.genotypeFPsc_trt5E_live.DEGs.int.rD.rR500.v3.0anno"                           
[46] "root.trt5E_live.genotypeFPsc.DEGs.int.rB.rR500.v3.0anno"                                      
[47] "root.trt5E_live.genotypeFPsc.DEGs.int.rD.rR500.v3.0anno"                                      
[48] "root.trt5E_live.genotypeR500_trt5E_live.DEGs.int.rB.rFPsc.v3.0anno"                           
[49] "root.trt5E_live.genotypeR500_trt5E_live.DEGs.int.rD.rFPsc.v3.0anno"                           
[50] "root.trt5E_live.genotypeR500.DEGs.int.rB.rFPsc.v3.0anno"                                      
# playing with map and lapply
DEG.count.list.e1.v3.0annotation.all %>% map(~filter(.,FDR<0.05)) # does work
$leaf.FPsc.trtlive.DEGs.all.rD.v3.0anno
# A tibble: 2 x 11
     X1 genes logFC logCPM    LR  PValue     FDR AGI   At_symbol
  <int> <chr> <dbl>  <dbl> <dbl>   <dbl>   <dbl> <chr> <chr>    
1     1 BraA…  2.06  0.119  28.2 1.10e-7 0.00256 AT3G… <NA>     
2     2 BraA…  2.44  0.460  24.1 9.03e-7 0.0105  AT1G… AtVTL1   
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>

$leaf.genotypeFPsc_trt5E_live.genotypeFPsc_trt5E_dead.genotypeFPsc.DEGs.int.rB.rR500.v3.0anno
# A tibble: 18,895 x 13
      X1 genes logFC.genotypeF… logFC.genotypeF… logFC.genotypeF… logCPM
   <int> <chr>            <dbl>            <dbl>            <dbl>  <dbl>
 1     1 BraA…            -13.1           1.28             1.76     6.28
 2     2 BraA…            -12.4           0.829            0.0153   6.99
 3     3 BraA…             12.1          -0.791            1.16     6.40
 4     4 BraA…            -12.1          -0.0737           0.114    5.28
 5     5 BraA…            -12.1          -0.201           -0.825    6.50
 6     6 BraA…            -12.0           1.20            -0.163    5.28
 7     7 BraA…            -11.8           2.08             2.81     4.84
 8     8 BraA…             11.7          -1.18            -0.702    6.97
 9     9 BraA…            -11.7          -0.149           -0.115    4.94
10    10 BraA…            -11.6           0.0524           0.0330   4.78
# ... with 18,885 more rows, and 7 more variables: LR <dbl>, PValue <dbl>,
#   FDR <dbl>, AGI <chr>, At_symbol <chr>, At_short_description <chr>,
#   perc_ID <dbl>

$leaf.genotypeFPsc_trt5E_live.genotypeFPsc_trtBLANK_NA.genotypeFPsc.DEGs.int.rD.rR500.v3.0anno
# A tibble: 18,895 x 13
      X1 genes logFC.genotypeF… logFC.genotypeF… logFC.genotypeF… logCPM
   <int> <chr>            <dbl>            <dbl>            <dbl>  <dbl>
 1     1 BraA…            -13.3           2.23             3.29     6.34
 2     2 BraA…             12.8          -1.76            -1.60     5.99
 3     3 BraA…            -12.3           0.201           -0.624    6.50
 4     4 BraA…            -12.2           0.0737           0.188    5.28
 5     5 BraA…             12.1          -1.17            -1.38     5.13
 6     6 BraA…            -11.9           1.27             1.98     5.04
 7     7 BraA…            -11.8           0.149            0.0341   4.94
 8     8 BraA…            -11.8          -1.28             0.481    6.28
 9     9 BraA…            -11.6          -0.0524          -0.0194   4.78
10    10 BraA…            -11.5          -0.829           -0.814    6.99
# ... with 18,885 more rows, and 7 more variables: LR <dbl>, PValue <dbl>,
#   FDR <dbl>, AGI <chr>, At_symbol <chr>, At_short_description <chr>,
#   perc_ID <dbl>

$leaf.genotypeFPsc.DEGs.add.rB.rR500.v3.0anno
# A tibble: 19,658 x 11
      X1 genes logFC logCPM    LR PValue   FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>  <dbl> <dbl> <chr> <chr>    
 1     1 BraA… -12.4   6.50 2505.      0     0 AT1G… TAR4     
 2     2 BraA… -12.1   5.28 4344.      0     0 <NA>  <NA>     
 3     3 BraA…  12.1   6.40 3411.      0     0 AT2G… ATCNGC11 
 4     4 BraA… -12.1   6.99 1955.      0     0 AT4G… CRK39    
 5     5 BraA… -11.9   6.28 1578.      0     0 AT1G… ATBBD1   
 6     6 BraA… -11.8   4.94 1986.      0     0 <NA>  <NA>     
 7     7 BraA… -11.6   4.78 3000.      0     0 <NA>  <NA>     
 8     8 BraA… -11.6   5.28 3458.      0     0 AT1G… <NA>     
 9     9 BraA… -11.5   4.63 2430.      0     0 AT5G… <NA>     
10    10 BraA…  11.4   5.99 5024.      0     0 <NA>  <NA>     
# ... with 19,648 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$leaf.genotypeFPsc.DEGs.add.rD.rR500.v3.0anno
# A tibble: 19,658 x 11
      X1 genes logFC logCPM    LR PValue   FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>  <dbl> <dbl> <chr> <chr>    
 1     1 BraA… -12.4   6.50 2505.      0     0 AT1G… TAR4     
 2     2 BraA… -12.1   5.28 4344.      0     0 <NA>  <NA>     
 3     3 BraA…  12.1   6.40 3411.      0     0 AT2G… ATCNGC11 
 4     4 BraA… -12.1   6.99 1955.      0     0 AT4G… CRK39    
 5     5 BraA… -11.9   6.28 1578.      0     0 AT1G… ATBBD1   
 6     6 BraA… -11.8   4.94 1986.      0     0 <NA>  <NA>     
 7     7 BraA… -11.6   4.78 3000.      0     0 <NA>  <NA>     
 8     8 BraA… -11.6   5.28 3458.      0     0 AT1G… <NA>     
 9     9 BraA… -11.5   4.63 2430.      0     0 AT5G… <NA>     
10    10 BraA…  11.4   5.99 5024.      0     0 <NA>  <NA>     
# ... with 19,648 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$leaf.genotypeR500_trt5E_live.genotypeR500_trt5E_dead.genotypeR500.DEGs.int.rB.rFPsc.v3.0anno
# A tibble: 18,895 x 13
      X1 genes logFC.genotypeR… logFC.genotypeR… logFC.genotypeR… logCPM
   <int> <chr>            <dbl>            <dbl>            <dbl>  <dbl>
 1     1 BraA…             13.1          -1.28            -1.76     6.28
 2     2 BraA…             12.4          -0.829           -0.0153   6.99
 3     3 BraA…            -12.1           0.791           -1.16     6.40
 4     4 BraA…             12.1           0.0737          -0.114    5.28
 5     5 BraA…             12.1           0.201            0.825    6.50
 6     6 BraA…             12.0          -1.20             0.163    5.28
 7     7 BraA…             11.8          -2.08            -2.81     4.84
 8     8 BraA…            -11.7           1.18             0.702    6.97
 9     9 BraA…             11.7           0.149            0.115    4.94
10    10 BraA…             11.6          -0.0524          -0.0330   4.78
# ... with 18,885 more rows, and 7 more variables: LR <dbl>, PValue <dbl>,
#   FDR <dbl>, AGI <chr>, At_symbol <chr>, At_short_description <chr>,
#   perc_ID <dbl>

$leaf.genotypeR500_trt5E_live.genotypeR500_trtBLANK_NA.genotypeR500.DEGs.int.rD.rFPsc.v3.0anno
# A tibble: 18,895 x 13
      X1 genes logFC.genotypeR… logFC.genotypeR… logFC.genotypeR… logCPM
   <int> <chr>            <dbl>            <dbl>            <dbl>  <dbl>
 1     1 BraA…             13.3          -2.23            -3.29     6.34
 2     2 BraA…            -12.8           1.76             1.60     5.99
 3     3 BraA…             12.3          -0.201            0.624    6.50
 4     4 BraA…             12.2          -0.0737          -0.188    5.28
 5     5 BraA…            -12.1           1.17             1.38     5.13
 6     6 BraA…             11.9          -1.27            -1.98     5.04
 7     7 BraA…             11.8          -0.149           -0.0341   4.94
 8     8 BraA…             11.8           1.28            -0.481    6.28
 9     9 BraA…             11.6           0.0524           0.0194   4.78
10    10 BraA…             11.5           0.829            0.814    6.99
# ... with 18,885 more rows, and 7 more variables: LR <dbl>, PValue <dbl>,
#   FDR <dbl>, AGI <chr>, At_symbol <chr>, At_short_description <chr>,
#   perc_ID <dbl>

$leaf.genotypeR500.DEGs.add.rB.rFPsc.v3.0anno
# A tibble: 19,658 x 11
      X1 genes logFC logCPM    LR PValue   FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>  <dbl> <dbl> <chr> <chr>    
 1     1 BraA…  12.4   6.50 2505.      0     0 AT1G… TAR4     
 2     2 BraA…  12.1   5.28 4344.      0     0 <NA>  <NA>     
 3     3 BraA… -12.1   6.40 3411.      0     0 AT2G… ATCNGC11 
 4     4 BraA…  12.1   6.99 1955.      0     0 AT4G… CRK39    
 5     5 BraA…  11.9   6.28 1578.      0     0 AT1G… ATBBD1   
 6     6 BraA…  11.8   4.94 1986.      0     0 <NA>  <NA>     
 7     7 BraA…  11.6   4.78 3000.      0     0 <NA>  <NA>     
 8     8 BraA…  11.6   5.28 3458.      0     0 AT1G… <NA>     
 9     9 BraA…  11.5   4.63 2430.      0     0 AT5G… <NA>     
10    10 BraA… -11.4   5.99 5024.      0     0 <NA>  <NA>     
# ... with 19,648 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$leaf.genotypeR500.DEGs.add.rD.rFPsc.v3.0anno
# A tibble: 19,658 x 11
      X1 genes logFC logCPM    LR PValue   FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>  <dbl> <dbl> <chr> <chr>    
 1     1 BraA…  12.4   6.50 2505.      0     0 AT1G… TAR4     
 2     2 BraA…  12.1   5.28 4344.      0     0 <NA>  <NA>     
 3     3 BraA… -12.1   6.40 3411.      0     0 AT2G… ATCNGC11 
 4     4 BraA…  12.1   6.99 1955.      0     0 AT4G… CRK39    
 5     5 BraA…  11.9   6.28 1578.      0     0 AT1G… ATBBD1   
 6     6 BraA…  11.8   4.94 1986.      0     0 <NA>  <NA>     
 7     7 BraA…  11.6   4.78 3000.      0     0 <NA>  <NA>     
 8     8 BraA…  11.6   5.28 3458.      0     0 AT1G… <NA>     
 9     9 BraA…  11.5   4.63 2430.      0     0 AT5G… <NA>     
10    10 BraA… -11.4   5.99 5024.      0     0 <NA>  <NA>     
# ... with 19,648 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$leaf.R500.trtlive.DEGs.all.rD.v3.0anno
# A tibble: 1,927 x 11
      X1 genes logFC logCPM    LR   PValue      FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>    <dbl>    <dbl> <chr> <chr>    
 1     1 BraA… -2.06   5.13  64.4 9.98e-16 2.40e-11 AT2G… ATP5CS   
 2     2 BraA… -1.55   5.25  42.0 9.02e-11 1.09e- 6 AT5G… AtcPT4   
 3     3 BraA… -1.67   2.22  37.2 1.04e- 9 8.35e- 6 AT1G… ATGSTU25 
 4     4 BraA… -1.18   3.93  36.1 1.86e- 9 1.12e- 5 AT2G… ANNAT4   
 5     5 BraA… -2.08   1.98  35.7 2.33e- 9 1.12e- 5 AT5G… <NA>     
 6     6 BraA…  2.53   3.65  34.3 4.63e- 9 1.86e- 5 AT3G… CYP72A8  
 7     7 BraA… -1.63   1.89  33.7 6.36e- 9 2.19e- 5 AT5G… <NA>     
 8     8 BraA… -1.94   7.40  32.9 9.50e- 9 2.86e- 5 AT3G… UGP3     
 9     9 BraA… -2.93   2.43  32.6 1.10e- 8 2.95e- 5 AT1G… AtPFA-DS…
10    10 BraA… -2.27   6.82  32.4 1.24e- 8 2.99e- 5 AT1G… ATPPCK1  
# ... with 1,917 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$leaf.trt5E_dead.DEGs.add.rB.rFPsc.v3.0anno
# A tibble: 0 x 11
# ... with 11 variables: X1 <int>, genes <chr>, logFC <dbl>, logCPM <dbl>,
#   LR <dbl>, PValue <dbl>, FDR <dbl>, AGI <chr>, At_symbol <chr>,
#   At_short_description <chr>, perc_ID <dbl>

$leaf.trt5E_dead.DEGs.add.rB.rR500.v3.0anno
# A tibble: 0 x 11
# ... with 11 variables: X1 <int>, genes <chr>, logFC <dbl>, logCPM <dbl>,
#   LR <dbl>, PValue <dbl>, FDR <dbl>, AGI <chr>, At_symbol <chr>,
#   At_short_description <chr>, perc_ID <dbl>

$leaf.trt5E_dead.genotypeFPsc_trt5E_dead.DEGs.int.rB.rR500.v3.0anno
# A tibble: 2 x 12
     X1 genes logFC.trt5E_dead logFC.genotypeF… logCPM    LR  PValue
  <int> <chr>            <dbl>            <dbl>  <dbl> <dbl>   <dbl>
1     1 BraA…             1.31            -1.19   4.33  30.4 2.49e-7
2     2 BraA…             5.60            -5.46   3.93  30.4 2.56e-7
# ... with 5 more variables: FDR <dbl>, AGI <chr>, At_symbol <chr>,
#   At_short_description <chr>, perc_ID <dbl>

$leaf.trt5E_dead.genotypeR500_trt5E_dead.DEGs.int.rB.rFPsc.v3.0anno
# A tibble: 2 x 12
     X1 genes logFC.trt5E_dead logFC.genotypeR… logCPM    LR  PValue
  <int> <chr>            <dbl>            <dbl>  <dbl> <dbl>   <dbl>
1     1 BraA…            0.124             1.19   4.33  30.4 2.49e-7
2     2 BraA…            0.142             5.46   3.93  30.4 2.56e-7
# ... with 5 more variables: FDR <dbl>, AGI <chr>, At_symbol <chr>,
#   At_short_description <chr>, perc_ID <dbl>

$leaf.trt5E_live.DEGs.add.rB.rFPsc.v3.0anno
# A tibble: 144 x 11
      X1 genes  logFC logCPM    LR  PValue     FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>   <dbl>   <dbl> <chr> <chr>    
 1     1 BraA…  0.617  3.31   29.9 4.54e-8 0.00114 AT1G… <NA>     
 2     2 BraA… -1.74   3.55   28.1 1.16e-7 0.00146 AT1G… AtWSCP   
 3     3 BraA…  0.579  3.07   24.4 7.75e-7 0.00619 AT5G… ATHIR1   
 4     4 BraA… -1.30   0.169  24.0 9.82e-7 0.00619 AT1G… GXM1     
 5     5 BraA… -0.573  5.72   22.0 2.77e-6 0.00936 AT1G… ADT1     
 6     6 BraA… -0.625  3.09   21.9 2.82e-6 0.00936 AT4G… GrxC5    
 7     7 BraA… -0.615  3.75   21.7 3.13e-6 0.00936 AT2G… ALF1     
 8     8 BraA… -1.63   2.99   21.7 3.26e-6 0.00936 AT1G… <NA>     
 9     9 BraA…  1.52  -0.158  21.6 3.34e-6 0.00936 AT4G… ATK5     
10    10 BraA… -0.550  3.01   20.9 4.91e-6 0.0124  AT5G… <NA>     
# ... with 134 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$leaf.trt5E_live.DEGs.add.rB.rR500.v3.0anno
# A tibble: 144 x 11
      X1 genes  logFC logCPM    LR  PValue     FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>   <dbl>   <dbl> <chr> <chr>    
 1     1 BraA…  0.617  3.31   29.9 4.54e-8 0.00114 AT1G… <NA>     
 2     2 BraA… -1.74   3.55   28.1 1.16e-7 0.00146 AT1G… AtWSCP   
 3     3 BraA…  0.579  3.07   24.4 7.75e-7 0.00619 AT5G… ATHIR1   
 4     4 BraA… -1.30   0.169  24.0 9.82e-7 0.00619 AT1G… GXM1     
 5     5 BraA… -0.573  5.72   22.0 2.77e-6 0.00936 AT1G… ADT1     
 6     6 BraA… -0.625  3.09   21.9 2.82e-6 0.00936 AT4G… GrxC5    
 7     7 BraA… -0.615  3.75   21.7 3.13e-6 0.00936 AT2G… ALF1     
 8     8 BraA… -1.63   2.99   21.7 3.26e-6 0.00936 AT1G… <NA>     
 9     9 BraA…  1.52  -0.158  21.6 3.34e-6 0.00936 AT4G… ATK5     
10    10 BraA… -0.550  3.01   20.9 4.91e-6 0.0124  AT5G… <NA>     
# ... with 134 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$leaf.trt5E_live.DEGs.add.rD.rFPsc.v3.0anno
# A tibble: 1,932 x 11
      X1 genes  logFC logCPM    LR   PValue     FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>    <dbl>   <dbl> <chr> <chr>    
 1     1 BraA… -1.63   1.26   38.1 6.58e-10 1.66e-5 AT1G… ATGSTU25 
 2     2 BraA… -1.88   3.55   32.3 1.29e- 8 1.44e-4 AT1G… AtWSCP   
 3     3 BraA… -0.737  3.75   31.1 2.45e- 8 1.44e-4 AT2G… ALF1     
 4     4 BraA…  1.25   0.725  31.0 2.56e- 8 1.44e-4 <NA>  <NA>     
 5     5 BraA…  0.889  5.15   30.8 2.85e- 8 1.44e-4 AT5G… <NA>     
 6     6 BraA…  0.841  3.81   30.2 3.85e- 8 1.62e-4 AT5G… <NA>     
 7     7 BraA…  1.44   1.69   29.8 4.91e- 8 1.77e-4 AT1G… SMR2     
 8     8 BraA…  1.80   1.28   27.9 1.26e- 7 3.96e-4 AT3G… <NA>     
 9     9 BraA…  0.537  3.28   27.6 1.51e- 7 4.22e-4 AT5G… ATFIP1[V]
10    10 BraA… -0.370  5.90   26.9 2.18e- 7 5.36e-4 AT1G… ARC12    
# ... with 1,922 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$leaf.trt5E_live.DEGs.add.rD.rR500.v3.0anno
# A tibble: 1,932 x 11
      X1 genes  logFC logCPM    LR   PValue     FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>    <dbl>   <dbl> <chr> <chr>    
 1     1 BraA… -1.63   1.26   38.1 6.58e-10 1.66e-5 AT1G… ATGSTU25 
 2     2 BraA… -1.88   3.55   32.3 1.29e- 8 1.44e-4 AT1G… AtWSCP   
 3     3 BraA… -0.737  3.75   31.1 2.45e- 8 1.44e-4 AT2G… ALF1     
 4     4 BraA…  1.25   0.725  31.0 2.56e- 8 1.44e-4 <NA>  <NA>     
 5     5 BraA…  0.889  5.15   30.8 2.85e- 8 1.44e-4 AT5G… <NA>     
 6     6 BraA…  0.841  3.81   30.2 3.85e- 8 1.62e-4 AT5G… <NA>     
 7     7 BraA…  1.44   1.69   29.8 4.91e- 8 1.77e-4 AT1G… SMR2     
 8     8 BraA…  1.80   1.28   27.9 1.26e- 7 3.96e-4 AT3G… <NA>     
 9     9 BraA…  0.537  3.28   27.6 1.51e- 7 4.22e-4 AT5G… ATFIP1[V]
10    10 BraA… -0.370  5.90   26.9 2.18e- 7 5.36e-4 AT1G… ARC12    
# ... with 1,922 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$leaf.trt5E_live.genotypeFPsc_trt5E_live.DEGs.int.rB.rR500.v3.0anno
# A tibble: 399 x 12
      X1 genes logFC.trt5E_live logFC.genotypeF… logCPM    LR   PValue
   <int> <chr>            <dbl>            <dbl>  <dbl> <dbl>    <dbl>
 1     1 BraA…           -1.44             1.44    3.15  45.2 1.53e-10
 2     2 BraA…           -0.107            4.00    1.98  37.2 8.22e- 9
 3     3 BraA…            0.503            0.261   3.31  31.4 1.53e- 7
 4     4 BraA…           -5.55             4.85    6.89  30.8 2.02e- 7
 5     5 BraA…           -2.03             2.06    3.23  30.4 2.55e- 7
 6     6 BraA…           -0.842            0.719   7.36  29.9 3.24e- 7
 7     7 BraA…           -1.26             1.05    4.67  29.8 3.32e- 7
 8     8 BraA…           -1.73             1.82    2.32  29.7 3.54e- 7
 9     9 BraA…            5.51            -5.39    3.93  29.1 4.72e- 7
10    10 BraA…           -1.77             1.82    3.55  28.3 7.33e- 7
# ... with 389 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$leaf.trt5E_live.genotypeFPsc_trt5E_live.DEGs.int.rD.rR500.v3.0anno
# A tibble: 2,061 x 12
      X1 genes logFC.trt5E_live logFC.genotypeF… logCPM    LR   PValue
   <int> <chr>            <dbl>            <dbl>  <dbl> <dbl>    <dbl>
 1     1 BraA…            -2.05            2.10    4.33  69.8 6.82e-16
 2     2 BraA…            -2.93            2.85    2.99  50.6 1.05e-11
 3     3 BraA…             1.36           -1.10    4.25  45.3 1.44e-10
 4     4 BraA…            -2.25            1.85    7.95  44.9 1.77e-10
 5     5 BraA…            -1.06            0.665   3.75  44.7 1.94e-10
 6     6 BraA…            -2.43            1.96    3.99  42.5 5.87e-10
 7     7 BraA…             2.36           -2.08    3.32  40.7 1.48e- 9
 8     8 BraA…             1.22           -0.692   5.15  38.5 4.34e- 9
 9     9 BraA…            -1.67            1.09    1.26  38.2 4.98e- 9
10    10 BraA…            -4.17            3.88    3.53  37.6 6.82e- 9
# ... with 2,051 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$leaf.trt5E_live.genotypeFPsc.DEGs.int.rB.rR500.v3.0anno
# A tibble: 5 x 11
     X1 genes logFC logCPM    LR  PValue     FDR AGI   At_symbol
  <int> <chr> <dbl>  <dbl> <dbl>   <dbl>   <dbl> <chr> <chr>    
1     1 BraA…  4.00   1.98  34.5 4.19e-9 1.06e-4 <NA>  <NA>     
2     2 BraA… -5.39   3.93  21.6 3.33e-6 2.89e-2 AT1G… ATU2AF65B
3     3 BraA…  1.44   3.15  21.6 3.43e-6 2.89e-2 AT1G… ASB1     
4     4 BraA… -4.43   2.62  20.2 7.13e-6 4.50e-2 AT2G… ATPEX10  
5     5 BraA…  2.41   2.99  19.6 9.72e-6 4.90e-2 AT1G… AtPFA-DS…
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>

$leaf.trt5E_live.genotypeFPsc.DEGs.int.rD.rR500.v3.0anno
# A tibble: 8 x 11
     X1 genes logFC logCPM    LR   PValue     FDR AGI   At_symbol
  <int> <chr> <dbl>  <dbl> <dbl>    <dbl>   <dbl> <chr> <chr>    
1     1 BraA…  2.10   4.33  35.4  2.65e-9 6.68e-5 AT2G… ATP5CS   
2     2 BraA…  3.21   2.98  31.8  1.72e-8 2.17e-4 AT5G… ABCF2    
3     3 BraA…  2.85   2.99  27.7  1.43e-7 1.20e-3 AT1G… AtPFA-DS…
4     4 BraA…  1.72   5.63  22.7  1.91e-6 1.20e-2 AT5G… AtcPT4   
5     5 BraA… -3.46   2.58  21.0  4.51e-6 2.27e-2 AT1G… ATGPT2   
6     6 BraA…  3.88   3.53  19.8  8.40e-6 3.53e-2 AT3G… ATACP5   
7     7 BraA… -2.08   3.32  19.5 10.00e-6 3.60e-2 AT5G… <NA>     
8     8 BraA…  2.81   1.29  19.0  1.31e-5 4.14e-2 AT5G… <NA>     
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>

$leaf.trt5E_live.genotypeR500_trt5E_live.DEGs.int.rB.rFPsc.v3.0anno
# A tibble: 399 x 12
      X1 genes logFC.trt5E_live logFC.genotypeR… logCPM    LR   PValue
   <int> <chr>            <dbl>            <dbl>  <dbl> <dbl>    <dbl>
 1     1 BraA…          0.00152           -1.44    3.15  45.2 1.53e-10
 2     2 BraA…          3.89              -4.00    1.98  37.2 8.22e- 9
 3     3 BraA…          0.764             -0.261   3.31  31.4 1.53e- 7
 4     4 BraA…         -0.695             -4.85    6.89  30.8 2.02e- 7
 5     5 BraA…          0.0355            -2.06    3.23  30.4 2.55e- 7
 6     6 BraA…         -0.123             -0.719   7.36  29.9 3.24e- 7
 7     7 BraA…         -0.209             -1.05    4.67  29.8 3.32e- 7
 8     8 BraA…          0.0889            -1.82    2.32  29.7 3.54e- 7
 9     9 BraA…          0.117              5.39    3.93  29.1 4.72e- 7
10    10 BraA…          0.0435            -1.82    3.55  28.3 7.33e- 7
# ... with 389 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$leaf.trt5E_live.genotypeR500_trt5E_live.DEGs.int.rD.rFPsc.v3.0anno
# A tibble: 2,061 x 12
      X1 genes logFC.trt5E_live logFC.genotypeR… logCPM    LR   PValue
   <int> <chr>            <dbl>            <dbl>  <dbl> <dbl>    <dbl>
 1     1 BraA…           0.0565           -2.10    4.33  69.8 6.82e-16
 2     2 BraA…          -0.0794           -2.85    2.99  50.6 1.05e-11
 3     3 BraA…           0.263             1.10    4.25  45.3 1.44e-10
 4     4 BraA…          -0.407            -1.85    7.95  44.9 1.77e-10
 5     5 BraA…          -0.393            -0.665   3.75  44.7 1.94e-10
 6     6 BraA…          -0.471            -1.96    3.99  42.5 5.87e-10
 7     7 BraA…           0.286             2.08    3.32  40.7 1.48e- 9
 8     8 BraA…           0.523             0.692   5.15  38.5 4.34e- 9
 9     9 BraA…          -0.583            -1.09    1.26  38.2 4.98e- 9
10    10 BraA…          -0.288            -3.88    3.53  37.6 6.82e- 9
# ... with 2,051 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$leaf.trt5E_live.genotypeR500.DEGs.int.rB.rFPsc.v3.0anno
# A tibble: 5 x 11
     X1 genes logFC logCPM    LR  PValue     FDR AGI   At_symbol
  <int> <chr> <dbl>  <dbl> <dbl>   <dbl>   <dbl> <chr> <chr>    
1     1 BraA… -4.00   1.98  34.5 4.19e-9 1.06e-4 <NA>  <NA>     
2     2 BraA…  5.39   3.93  21.6 3.33e-6 2.89e-2 AT1G… ATU2AF65B
3     3 BraA… -1.44   3.15  21.6 3.43e-6 2.89e-2 AT1G… ASB1     
4     4 BraA…  4.43   2.62  20.2 7.13e-6 4.50e-2 AT2G… ATPEX10  
5     5 BraA… -2.41   2.99  19.6 9.72e-6 4.90e-2 AT1G… AtPFA-DS…
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>

$root.FPsc.trtlive.DEGs.all.rD.v3.0anno
# A tibble: 9 x 11
     X1 genes  logFC logCPM    LR   PValue     FDR AGI   At_symbol
  <int> <chr>  <dbl>  <dbl> <dbl>    <dbl>   <dbl> <chr> <chr>    
1     1 BraA… -1.70   5.74   37.9 7.54e-10 1.99e-5 AT1G… <NA>     
2     2 BraA… -2.70   0.746  27.1 1.92e- 7 2.53e-3 AT5G… CGLD27   
3     3 BraA…  4.90   4.78   24.9 6.18e- 7 5.43e-3 AT5G… HSP18.2  
4     4 BraA…  3.02   4.43   21.3 3.97e- 6 2.27e-2 AT5G… HSP18.2  
5     5 BraA… -1.05   7.43   21.1 4.30e- 6 2.27e-2 AT1G… ATOPR2   
6     6 BraA… -0.761  2.51   20.6 5.79e- 6 2.43e-2 AT1G… <NA>     
7     7 BraA…  2.53   0.780  20.3 6.46e- 6 2.43e-2 AT3G… <NA>     
8     8 BraA… -1.31   3.16   19.5 9.87e- 6 2.96e-2 AT3G… BHLH039  
9     9 BraA… -0.938  6.99   19.5 1.01e- 5 2.96e-2 AT3G… AtDJ1A   
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>

$root.genotypeFPsc_trt5E_live.genotypeFPsc_trt5E_dead.genotypeFPsc.DEGs.int.rB.rR500.v3.0anno
# A tibble: 17,373 x 13
      X1 genes logFC.genotypeF… logFC.genotypeF… logFC.genotypeF… logCPM
   <int> <chr>            <dbl>            <dbl>            <dbl>  <dbl>
 1     1 BraA…             14.4          -2.48            -2.08     7.57
 2     2 BraA…            -14.3           1.08             1.42     7.50
 3     3 BraA…             13.6          -1.30            -0.0224   6.77
 4     4 BraA…             13.0          -1.33            -1.99     6.18
 5     5 BraA…            -12.6           2.16             2.96     5.81
 6     6 BraA…             12.5          -4.21            -4.13     5.83
 7     7 BraA…             12.3          -0.131           -1.29     5.50
 8     8 BraA…             12.3          -1.42            -0.269    5.36
 9     9 BraA…             12.2           0.0831          -1.14     5.49
10    10 BraA…             12.1          -0.139           -2.13     5.21
# ... with 17,363 more rows, and 7 more variables: LR <dbl>, PValue <dbl>,
#   FDR <dbl>, AGI <chr>, At_symbol <chr>, At_short_description <chr>,
#   perc_ID <dbl>

$root.genotypeFPsc_trt5E_live.genotypeFPsc_trtBLANK_NA.genotypeFPsc.DEGs.int.rD.rR500.v3.0anno
# A tibble: 17,373 x 13
      X1 genes logFC.genotypeF… logFC.genotypeF… logFC.genotypeF… logCPM
   <int> <chr>            <dbl>            <dbl>            <dbl>  <dbl>
 1     1 BraA…             13.3          -1.28             0.0181   6.55
 2     2 BraA…            -13.2          -1.08             0.338    7.50
 3     3 BraA…            -13.2           1.76             1.23     6.43
 4     4 BraA…            -12.5           0.465            1.32     7.08
 5     5 BraA…             12.3          -0.0831          -1.22     5.49
 6     6 BraA…             12.2           1.30             1.28     6.77
 7     7 BraA…             12.2           0.131           -1.16     5.50
 8     8 BraA…            -12.0           1.24             1.70     5.33
 9     9 BraA…             12.0           0.139           -1.99     5.21
10    10 BraA…             11.9           2.48             0.395    7.57
# ... with 17,363 more rows, and 7 more variables: LR <dbl>, PValue <dbl>,
#   FDR <dbl>, AGI <chr>, At_symbol <chr>, At_short_description <chr>,
#   perc_ID <dbl>

$root.genotypeFPsc.DEGs.add.rB.rR500.v3.0anno
# A tibble: 18,989 x 11
      X1 genes logFC logCPM    LR PValue   FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>  <dbl> <dbl> <chr> <chr>    
 1     1 BraA… -13.4   7.50 3038.      0     0 AT1G… <NA>     
 2     2 BraA…  13.0   6.77 1714.      0     0 <NA>  <NA>     
 3     3 BraA…  12.8   6.55 5105.      0     0 <NA>  <NA>     
 4     4 BraA…  12.6   7.57 2909.      0     0 AT2G… <NA>     
 5     5 BraA… -12.0   6.43 5449.      0     0 <NA>  <NA>     
 6     6 BraA… -11.8   7.08 3622.      0     0 AT3G… <NA>     
 7     7 BraA…  11.7   5.50 3920.      0     0 <NA>  <NA>     
 8     8 BraA…  11.7   5.49 3480.      0     0 <NA>  <NA>     
 9     9 BraA…  11.7   6.18 3861.      0     0 AT5G… <NA>     
10    10 BraA…  11.6   5.36 2391.      0     0 <NA>  <NA>     
# ... with 18,979 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.genotypeFPsc.DEGs.add.rD.rR500.v3.0anno
# A tibble: 18,989 x 11
      X1 genes logFC logCPM    LR PValue   FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>  <dbl> <dbl> <chr> <chr>    
 1     1 BraA… -13.4   7.50 3038.      0     0 AT1G… <NA>     
 2     2 BraA…  13.0   6.77 1714.      0     0 <NA>  <NA>     
 3     3 BraA…  12.8   6.55 5105.      0     0 <NA>  <NA>     
 4     4 BraA…  12.6   7.57 2909.      0     0 AT2G… <NA>     
 5     5 BraA… -12.0   6.43 5449.      0     0 <NA>  <NA>     
 6     6 BraA… -11.8   7.08 3622.      0     0 AT3G… <NA>     
 7     7 BraA…  11.7   5.50 3920.      0     0 <NA>  <NA>     
 8     8 BraA…  11.7   5.49 3480.      0     0 <NA>  <NA>     
 9     9 BraA…  11.7   6.18 3861.      0     0 AT5G… <NA>     
10    10 BraA…  11.6   5.36 2391.      0     0 <NA>  <NA>     
# ... with 18,979 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.genotypeR500_trt5E_live.genotypeR500_trt5E_dead.genotypeR500.DEGs.int.rB.rFPsc.v3.0anno
# A tibble: 17,373 x 13
      X1 genes logFC.genotypeR… logFC.genotypeR… logFC.genotypeR… logCPM
   <int> <chr>            <dbl>            <dbl>            <dbl>  <dbl>
 1     1 BraA…            -14.4           2.48             2.08     7.57
 2     2 BraA…             14.3          -1.08            -1.42     7.50
 3     3 BraA…            -13.6           1.30             0.0224   6.77
 4     4 BraA…            -13.0           1.33             1.99     6.18
 5     5 BraA…             12.6          -2.16            -2.96     5.81
 6     6 BraA…            -12.5           4.21             4.13     5.83
 7     7 BraA…            -12.3           0.131            1.29     5.50
 8     8 BraA…            -12.3           1.42             0.269    5.36
 9     9 BraA…            -12.2          -0.0831           1.14     5.49
10    10 BraA…            -12.1           0.139            2.13     5.21
# ... with 17,363 more rows, and 7 more variables: LR <dbl>, PValue <dbl>,
#   FDR <dbl>, AGI <chr>, At_symbol <chr>, At_short_description <chr>,
#   perc_ID <dbl>

$root.genotypeR500_trt5E_live.genotypeR500_trtBLANK_NA.genotypeR500.DEGs.int.rD.rFPsc.v3.0anno
# A tibble: 17,373 x 13
      X1 genes logFC.genotypeR… logFC.genotypeR… logFC.genotypeR… logCPM
   <int> <chr>            <dbl>            <dbl>            <dbl>  <dbl>
 1     1 BraA…            -13.3           1.28            -0.0181   6.55
 2     2 BraA…             13.2           1.08            -0.338    7.50
 3     3 BraA…             13.2          -1.76            -1.23     6.43
 4     4 BraA…             12.5          -0.465           -1.32     7.08
 5     5 BraA…            -12.3           0.0831           1.22     5.49
 6     6 BraA…            -12.2          -1.30            -1.28     6.77
 7     7 BraA…            -12.2          -0.131            1.16     5.50
 8     8 BraA…             12.0          -1.24            -1.70     5.33
 9     9 BraA…            -12.0          -0.139            1.99     5.21
10    10 BraA…            -11.9          -2.48            -0.395    7.57
# ... with 17,363 more rows, and 7 more variables: LR <dbl>, PValue <dbl>,
#   FDR <dbl>, AGI <chr>, At_symbol <chr>, At_short_description <chr>,
#   perc_ID <dbl>

$root.genotypeR500.DEGs.add.rB.rFPsc.v3.0anno
# A tibble: 18,989 x 11
      X1 genes logFC logCPM    LR PValue   FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>  <dbl> <dbl> <chr> <chr>    
 1     1 BraA…  13.4   7.50 3038.      0     0 AT1G… <NA>     
 2     2 BraA… -13.0   6.77 1714.      0     0 <NA>  <NA>     
 3     3 BraA… -12.8   6.55 5105.      0     0 <NA>  <NA>     
 4     4 BraA… -12.6   7.57 2909.      0     0 AT2G… <NA>     
 5     5 BraA…  12.0   6.43 5449.      0     0 <NA>  <NA>     
 6     6 BraA…  11.8   7.08 3622.      0     0 AT3G… <NA>     
 7     7 BraA… -11.7   5.50 3920.      0     0 <NA>  <NA>     
 8     8 BraA… -11.7   5.49 3480.      0     0 <NA>  <NA>     
 9     9 BraA… -11.7   6.18 3861.      0     0 AT5G… <NA>     
10    10 BraA… -11.6   5.36 2391.      0     0 <NA>  <NA>     
# ... with 18,979 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.genotypeR500.DEGs.add.rD.rFPsc.v3.0anno
# A tibble: 18,989 x 11
      X1 genes logFC logCPM    LR PValue   FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>  <dbl> <dbl> <chr> <chr>    
 1     1 BraA…  13.4   7.50 3038.      0     0 AT1G… <NA>     
 2     2 BraA… -13.0   6.77 1714.      0     0 <NA>  <NA>     
 3     3 BraA… -12.8   6.55 5105.      0     0 <NA>  <NA>     
 4     4 BraA… -12.6   7.57 2909.      0     0 AT2G… <NA>     
 5     5 BraA…  12.0   6.43 5449.      0     0 <NA>  <NA>     
 6     6 BraA…  11.8   7.08 3622.      0     0 AT3G… <NA>     
 7     7 BraA… -11.7   5.50 3920.      0     0 <NA>  <NA>     
 8     8 BraA… -11.7   5.49 3480.      0     0 <NA>  <NA>     
 9     9 BraA… -11.7   6.18 3861.      0     0 AT5G… <NA>     
10    10 BraA… -11.6   5.36 2391.      0     0 <NA>  <NA>     
# ... with 18,979 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.R500.trtlive.DEGs.all.rD.v3.0anno
# A tibble: 383 x 11
      X1 genes  logFC logCPM    LR  PValue     FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>   <dbl>   <dbl> <chr> <chr>    
 1     1 BraA…  1.26    4.60  33.9 5.82e-9 1.55e-4 AT1G… NLP4     
 2     2 BraA…  2.13    3.39  32.5 1.20e-8 1.60e-4 AT1G… <NA>     
 3     3 BraA…  2.23    1.67  31.4 2.05e-8 1.83e-4 AT3G… ABCA3    
 4     4 BraA…  1.70    3.81  30.6 3.14e-8 1.93e-4 AT3G… NF-YA6   
 5     5 BraA… -1.53    4.64  30.3 3.61e-8 1.93e-4 AT4G… <NA>     
 6     6 BraA…  1.28    3.98  29.2 6.42e-8 2.86e-4 AT5G… GLN1;4   
 7     7 BraA… -1.14    5.84  28.4 1.00e-7 3.29e-4 AT1G… AtNIGT1  
 8     8 BraA…  0.988   5.18  28.2 1.09e-7 3.29e-4 AT5G… <NA>     
 9     9 BraA…  1.77    5.64  28.2 1.12e-7 3.29e-4 AT5G… ATDUR3   
10    10 BraA… -1.37    3.74  27.9 1.30e-7 3.29e-4 AT1G… AtNIGT1  
# ... with 373 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.trt5E_dead.DEGs.add.rB.rFPsc.v3.0anno
# A tibble: 23 x 11
      X1 genes  logFC  logCPM    LR  PValue     FDR AGI   At_symbol
   <int> <chr>  <dbl>   <dbl> <dbl>   <dbl>   <dbl> <chr> <chr>    
 1     1 BraA…  1.42   2.28    32.0 1.53e-8 4.27e-4 AT5G… <NA>     
 2     2 BraA…  1.99   1.62    26.6 2.46e-7 3.43e-3 AT4G… CYP82C4  
 3     3 BraA…  0.941  2.67    24.2 8.86e-7 7.05e-3 AT3G… <NA>     
 4     4 BraA…  1.81   1.53    23.9 1.01e-6 7.05e-3 AT4G… ATIRT1   
 5     5 BraA…  1.67   0.0566  20.8 5.15e-6 2.73e-2 AT1G… <NA>     
 6     6 BraA…  1.43   0.469   20.5 5.87e-6 2.73e-2 AT2G… Iqd4     
 7     7 BraA…  1.42   2.16    19.9 8.24e-6 3.28e-2 AT2G… <NA>     
 8     8 BraA…  1.45   3.39    19.5 1.02e-5 3.28e-2 AT5G… <NA>     
 9     9 BraA…  1.47   2.36    19.2 1.16e-5 3.28e-2 AT5G… ATPT4    
10    10 BraA… -4.78  -0.507   19.1 1.26e-5 3.28e-2 <NA>  <NA>     
# ... with 13 more rows, and 2 more variables: At_short_description <chr>,
#   perc_ID <dbl>

$root.trt5E_dead.DEGs.add.rB.rR500.v3.0anno
# A tibble: 23 x 11
      X1 genes  logFC  logCPM    LR  PValue     FDR AGI   At_symbol
   <int> <chr>  <dbl>   <dbl> <dbl>   <dbl>   <dbl> <chr> <chr>    
 1     1 BraA…  1.42   2.28    32.0 1.53e-8 4.27e-4 AT5G… <NA>     
 2     2 BraA…  1.99   1.62    26.6 2.46e-7 3.43e-3 AT4G… CYP82C4  
 3     3 BraA…  0.941  2.67    24.2 8.86e-7 7.05e-3 AT3G… <NA>     
 4     4 BraA…  1.81   1.53    23.9 1.01e-6 7.05e-3 AT4G… ATIRT1   
 5     5 BraA…  1.67   0.0566  20.8 5.15e-6 2.73e-2 AT1G… <NA>     
 6     6 BraA…  1.43   0.469   20.5 5.87e-6 2.73e-2 AT2G… Iqd4     
 7     7 BraA…  1.42   2.16    19.9 8.24e-6 3.28e-2 AT2G… <NA>     
 8     8 BraA…  1.45   3.39    19.5 1.02e-5 3.28e-2 AT5G… <NA>     
 9     9 BraA…  1.47   2.36    19.2 1.16e-5 3.28e-2 AT5G… ATPT4    
10    10 BraA… -4.78  -0.507   19.1 1.26e-5 3.28e-2 <NA>  <NA>     
# ... with 13 more rows, and 2 more variables: At_short_description <chr>,
#   perc_ID <dbl>

$root.trt5E_dead.genotypeFPsc_trt5E_dead.DEGs.int.rB.rR500.v3.0anno
# A tibble: 40 x 12
      X1 genes logFC.trt5E_dead logFC.genotypeF… logCPM    LR  PValue
   <int> <chr>            <dbl>            <dbl>  <dbl> <dbl>   <dbl>
 1     1 BraA…          -0.0755           2.15    6.68   39.4 2.73e-9
 2     2 BraA…           0.797            1.55    1.62   37.3 8.04e-9
 3     3 BraA…           1.41             0.0163  2.28   30.9 1.99e-7
 4     4 BraA…           0.882            1.65    1.59   28.4 6.96e-7
 5     5 BraA…           0.770            1.39    3.39   27.0 1.38e-6
 6     6 BraA…          -0.174            1.33    2.87   26.4 1.82e-6
 7     7 BraA…          -0.0525          -3.86    2.45   26.3 1.93e-6
 8     8 BraA…           0.143            2.27    2.81   24.9 3.94e-6
 9     9 BraA…           0.901            1.15    0.469  24.2 5.61e-6
10    10 BraA…           0.0770           1.36    9.03   23.6 7.66e-6
# ... with 30 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$root.trt5E_dead.genotypeR500_trt5E_dead.DEGs.int.rB.rFPsc.v3.0anno
# A tibble: 40 x 12
      X1 genes logFC.trt5E_dead logFC.genotypeR… logCPM    LR  PValue
   <int> <chr>            <dbl>            <dbl>  <dbl> <dbl>   <dbl>
 1     1 BraA…             2.07          -2.15    6.68   39.4 2.73e-9
 2     2 BraA…             2.35          -1.55    1.62   37.3 8.04e-9
 3     3 BraA…             1.42          -0.0163  2.28   30.9 1.99e-7
 4     4 BraA…             2.53          -1.65    1.59   28.4 6.96e-7
 5     5 BraA…             2.16          -1.39    3.39   27.0 1.38e-6
 6     6 BraA…             1.16          -1.33    2.87   26.4 1.82e-6
 7     7 BraA…            -3.92           3.86    2.45   26.3 1.93e-6
 8     8 BraA…             2.41          -2.27    2.81   24.9 3.94e-6
 9     9 BraA…             2.06          -1.15    0.469  24.2 5.61e-6
10    10 BraA…             1.44          -1.36    9.03   23.6 7.66e-6
# ... with 30 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$root.trt5E_live.DEGs.add.rB.rFPsc.v3.0anno
# A tibble: 931 x 11
      X1 genes  logFC logCPM    LR   PValue     FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>    <dbl>   <dbl> <chr> <chr>    
 1     1 BraA… -1.28   2.79   48.3 3.58e-12 9.97e-8 AT2G… <NA>     
 2     2 BraA… -0.853  7.44   39.7 2.94e-10 4.10e-6 AT3G… AtDJ1A   
 3     3 BraA… -1.01   5.65   38.3 6.09e-10 5.66e-6 AT1G… AtNIGT1  
 4     4 BraA… -0.728  6.87   36.3 1.71e- 9 1.19e-5 AT3G… AtDJ1A   
 5     5 BraA…  1.11   3.16   33.4 7.41e- 9 4.13e-5 AT4G… AAT1     
 6     6 BraA…  2.09   1.69   32.9 9.58e- 9 4.45e-5 AT1G… PHT1;8   
 7     7 BraA…  1.41   0.714  30.2 3.96e- 8 1.58e-4 AT1G… <NA>     
 8     8 BraA…  1.30   2.16   29.4 5.96e- 8 2.08e-4 AT5G… AtMYB19  
 9     9 BraA…  1.12   1.66   28.4 9.71e- 8 2.49e-4 AT4G… <NA>     
10    10 BraA…  1.23   3.30   28.3 1.02e- 7 2.49e-4 AT3G… LAC7     
# ... with 921 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.trt5E_live.DEGs.add.rB.rR500.v3.0anno
# A tibble: 931 x 11
      X1 genes  logFC logCPM    LR   PValue     FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>    <dbl>   <dbl> <chr> <chr>    
 1     1 BraA… -1.28   2.79   48.3 3.58e-12 9.97e-8 AT2G… <NA>     
 2     2 BraA… -0.853  7.44   39.7 2.94e-10 4.10e-6 AT3G… AtDJ1A   
 3     3 BraA… -1.01   5.65   38.3 6.09e-10 5.66e-6 AT1G… AtNIGT1  
 4     4 BraA… -0.728  6.87   36.3 1.71e- 9 1.19e-5 AT3G… AtDJ1A   
 5     5 BraA…  1.11   3.16   33.4 7.41e- 9 4.13e-5 AT4G… AAT1     
 6     6 BraA…  2.09   1.69   32.9 9.58e- 9 4.45e-5 AT1G… PHT1;8   
 7     7 BraA…  1.41   0.714  30.2 3.96e- 8 1.58e-4 AT1G… <NA>     
 8     8 BraA…  1.30   2.16   29.4 5.96e- 8 2.08e-4 AT5G… AtMYB19  
 9     9 BraA…  1.12   1.66   28.4 9.71e- 8 2.49e-4 AT4G… <NA>     
10    10 BraA…  1.23   3.30   28.3 1.02e- 7 2.49e-4 AT3G… LAC7     
# ... with 921 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.trt5E_live.DEGs.add.rD.rFPsc.v3.0anno
# A tibble: 26 x 11
      X1 genes  logFC logCPM    LR  PValue     FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>   <dbl>   <dbl> <chr> <chr>    
 1     1 BraA… -1.37    2.49  35.6 2.39e-9 6.66e-5 AT3G… BHLH039  
 2     2 BraA… -1.38    1.82  31.6 1.93e-8 2.20e-4 AT3G… BHLH039  
 3     3 BraA… -0.754   7.44  31.2 2.37e-8 2.20e-4 AT3G… AtDJ1A   
 4     4 BraA… -0.648   6.87  28.8 7.97e-8 5.56e-4 AT3G… AtDJ1A   
 5     5 BraA… -0.600   5.31  27.9 1.30e-7 7.24e-4 AT4G… UGT73B1  
 6     6 BraA… -0.616   5.60  27.0 2.02e-7 9.37e-4 AT4G… UGT73B1  
 7     7 BraA…  1.21    2.58  26.2 3.10e-7 1.04e-3 AT1G… TAR4     
 8     8 BraA… -0.831   5.65  26.1 3.26e-7 1.04e-3 AT1G… AtNIGT1  
 9     9 BraA…  1.69    3.06  26.0 3.37e-7 1.04e-3 AT1G… <NA>     
10    10 BraA… -1.10    7.15  24.8 6.25e-7 1.74e-3 AT1G… <NA>     
# ... with 16 more rows, and 2 more variables: At_short_description <chr>,
#   perc_ID <dbl>

$root.trt5E_live.DEGs.add.rD.rR500.v3.0anno
# A tibble: 26 x 11
      X1 genes  logFC logCPM    LR  PValue     FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>   <dbl>   <dbl> <chr> <chr>    
 1     1 BraA… -1.37    2.49  35.6 2.39e-9 6.66e-5 AT3G… BHLH039  
 2     2 BraA… -1.38    1.82  31.6 1.93e-8 2.20e-4 AT3G… BHLH039  
 3     3 BraA… -0.754   7.44  31.2 2.37e-8 2.20e-4 AT3G… AtDJ1A   
 4     4 BraA… -0.648   6.87  28.8 7.97e-8 5.56e-4 AT3G… AtDJ1A   
 5     5 BraA… -0.600   5.31  27.9 1.30e-7 7.24e-4 AT4G… UGT73B1  
 6     6 BraA… -0.616   5.60  27.0 2.02e-7 9.37e-4 AT4G… UGT73B1  
 7     7 BraA…  1.21    2.58  26.2 3.10e-7 1.04e-3 AT1G… TAR4     
 8     8 BraA… -0.831   5.65  26.1 3.26e-7 1.04e-3 AT1G… AtNIGT1  
 9     9 BraA…  1.69    3.06  26.0 3.37e-7 1.04e-3 AT1G… <NA>     
10    10 BraA… -1.10    7.15  24.8 6.25e-7 1.74e-3 AT1G… <NA>     
# ... with 16 more rows, and 2 more variables: At_short_description <chr>,
#   perc_ID <dbl>

$root.trt5E_live.genotypeFPsc_trt5E_live.DEGs.int.rB.rR500.v3.0anno
# A tibble: 608 x 12
      X1 genes logFC.trt5E_live logFC.genotypeF… logCPM    LR   PValue
   <int> <chr>            <dbl>            <dbl>  <dbl> <dbl>    <dbl>
 1     1 BraA…           -1.45             0.859   5.65  53.8 2.04e-12
 2     2 BraA…           -1.55             0.526   2.79  53.2 2.87e-12
 3     3 BraA…           -0.697           -1.05    7.15  44.3 2.45e-10
 4     4 BraA…           -0.663           -0.389   7.44  42.9 4.75e-10
 5     5 BraA…           -0.556           -0.349   6.87  38.8 3.76e- 9
 6     6 BraA…            1.06             1.83    1.59  38.6 4.18e- 9
 7     7 BraA…            1.73            -0.931   2.16  38.6 4.25e- 9
 8     8 BraA…            0.900            0.654   3.16  37.9 5.79e- 9
 9     9 BraA…            0.946            1.34    5.01  36.4 1.23e- 8
10    10 BraA…            0.527            0.753   4.69  35.9 1.61e- 8
# ... with 598 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$root.trt5E_live.genotypeFPsc_trt5E_live.DEGs.int.rD.rR500.v3.0anno
# A tibble: 77 x 12
      X1 genes logFC.trt5E_live logFC.genotypeF… logCPM    LR   PValue
   <int> <chr>            <dbl>            <dbl>  <dbl> <dbl>    <dbl>
 1     1 BraA…           -0.538           -1.21   7.15   41.7 8.66e-10
 2     2 BraA…           -1.14             0.590  5.65   35.9 1.59e- 8
 3     3 BraA…           -1.50             0.191  2.49   35.1 2.43e- 8
 4     4 BraA…           -0.581           -0.358  7.44   33.9 4.30e- 8
 5     5 BraA…            2.22            -2.33   1.23   33.7 4.91e- 8
 6     6 BraA…            1.57            -1.36   4.01   31.8 1.26e- 7
 7     7 BraA…           -0.836           -1.91   0.848  31.7 1.32e- 7
 8     8 BraA…           -1.58             0.333  1.82   31.2 1.66e- 7
 9     9 BraA…           -0.529           -0.246  6.87   30.4 2.55e- 7
10    10 BraA…            1.69            -1.46   3.49   29.9 3.29e- 7
# ... with 67 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$root.trt5E_live.genotypeFPsc.DEGs.int.rB.rR500.v3.0anno
# A tibble: 4 x 11
     X1 genes logFC logCPM    LR  PValue     FDR AGI   At_symbol
  <int> <chr> <dbl>  <dbl> <dbl>   <dbl>   <dbl> <chr> <chr>    
1     1 BraA… -4.86  4.91   25.7 3.90e-7 0.00548 AT1G… ATU2AF65B
2     2 BraA…  3.42  0.428  25.7 3.93e-7 0.00548 AT5G… <NA>     
3     3 BraA… -1.55  1.93   20.4 6.29e-6 0.0453  AT4G… UBC17    
4     4 BraA…  2.02  6.68   20.3 6.50e-6 0.0453  AT4G… <NA>     
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>

$root.trt5E_live.genotypeFPsc.DEGs.int.rD.rR500.v3.0anno
# A tibble: 2 x 11
     X1 genes logFC logCPM    LR  PValue    FDR AGI   At_symbol
  <int> <chr> <dbl>  <dbl> <dbl>   <dbl>  <dbl> <chr> <chr>    
1     1 BraA…  3.28  1.39   23.8 1.05e-6 0.0293 AT3G… <NA>     
2     2 BraA…  2.95  0.428  21.5 3.55e-6 0.0495 AT5G… <NA>     
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>

$root.trt5E_live.genotypeR500_trt5E_live.DEGs.int.rB.rFPsc.v3.0anno
# A tibble: 608 x 12
      X1 genes logFC.trt5E_live logFC.genotypeR… logCPM    LR   PValue
   <int> <chr>            <dbl>            <dbl>  <dbl> <dbl>    <dbl>
 1     1 BraA…           -0.590           -0.859   5.65  53.8 2.04e-12
 2     2 BraA…           -1.03            -0.526   2.79  53.2 2.87e-12
 3     3 BraA…           -1.74             1.05    7.15  44.3 2.45e-10
 4     4 BraA…           -1.05             0.389   7.44  42.9 4.75e-10
 5     5 BraA…           -0.905            0.349   6.87  38.8 3.76e- 9
 6     6 BraA…            2.89            -1.83    1.59  38.6 4.18e- 9
 7     7 BraA…            0.799            0.931   2.16  38.6 4.25e- 9
 8     8 BraA…            1.55            -0.654   3.16  37.9 5.79e- 9
 9     9 BraA…            2.29            -1.34    5.01  36.4 1.23e- 8
10    10 BraA…            1.28            -0.753   4.69  35.9 1.61e- 8
# ... with 598 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$root.trt5E_live.genotypeR500_trt5E_live.DEGs.int.rD.rFPsc.v3.0anno
# A tibble: 77 x 12
      X1 genes logFC.trt5E_live logFC.genotypeR… logCPM    LR   PValue
   <int> <chr>            <dbl>            <dbl>  <dbl> <dbl>    <dbl>
 1     1 BraA…           -1.75             1.21   7.15   41.7 8.66e-10
 2     2 BraA…           -0.554           -0.590  5.65   35.9 1.59e- 8
 3     3 BraA…           -1.31            -0.191  2.49   35.1 2.43e- 8
 4     4 BraA…           -0.939            0.358  7.44   33.9 4.30e- 8
 5     5 BraA…           -0.113            2.33   1.23   33.7 4.91e- 8
 6     6 BraA…            0.211            1.36   4.01   31.8 1.26e- 7
 7     7 BraA…           -2.75             1.91   0.848  31.7 1.32e- 7
 8     8 BraA…           -1.25            -0.333  1.82   31.2 1.66e- 7
 9     9 BraA…           -0.775            0.246  6.87   30.4 2.55e- 7
10    10 BraA…            0.236            1.46   3.49   29.9 3.29e- 7
# ... with 67 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$root.trt5E_live.genotypeR500.DEGs.int.rB.rFPsc.v3.0anno
# A tibble: 4 x 11
     X1 genes logFC logCPM    LR  PValue     FDR AGI   At_symbol
  <int> <chr> <dbl>  <dbl> <dbl>   <dbl>   <dbl> <chr> <chr>    
1     1 BraA…  4.86  4.91   25.7 3.90e-7 0.00548 AT1G… ATU2AF65B
2     2 BraA… -3.42  0.428  25.7 3.93e-7 0.00548 AT5G… <NA>     
3     3 BraA…  1.55  1.93   20.4 6.29e-6 0.0453  AT4G… UBC17    
4     4 BraA… -2.02  6.68   20.3 6.50e-6 0.0453  AT4G… <NA>     
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>
DEG.count.list.e1.v3.0annotation.all %>% map(nrow) # does work
$leaf.FPsc.trtlive.DEGs.all.rD.v3.0anno
[1] 23327

$leaf.genotypeFPsc_trt5E_live.genotypeFPsc_trt5E_dead.genotypeFPsc.DEGs.int.rB.rR500.v3.0anno
[1] 25210

$leaf.genotypeFPsc_trt5E_live.genotypeFPsc_trtBLANK_NA.genotypeFPsc.DEGs.int.rD.rR500.v3.0anno
[1] 25210

$leaf.genotypeFPsc.DEGs.add.rB.rR500.v3.0anno
[1] 25210

$leaf.genotypeFPsc.DEGs.add.rD.rR500.v3.0anno
[1] 25210

$leaf.genotypeR500_trt5E_live.genotypeR500_trt5E_dead.genotypeR500.DEGs.int.rB.rFPsc.v3.0anno
[1] 25210

$leaf.genotypeR500_trt5E_live.genotypeR500_trtBLANK_NA.genotypeR500.DEGs.int.rD.rFPsc.v3.0anno
[1] 25210

$leaf.genotypeR500.DEGs.add.rB.rFPsc.v3.0anno
[1] 25210

$leaf.genotypeR500.DEGs.add.rD.rFPsc.v3.0anno
[1] 25210

$leaf.R500.trtlive.DEGs.all.rD.v3.0anno
[1] 24087

$leaf.trt5E_dead.DEGs.add.rB.rFPsc.v3.0anno
[1] 25210

$leaf.trt5E_dead.DEGs.add.rB.rR500.v3.0anno
[1] 25210

$leaf.trt5E_dead.genotypeFPsc_trt5E_dead.DEGs.int.rB.rR500.v3.0anno
[1] 25210

$leaf.trt5E_dead.genotypeR500_trt5E_dead.DEGs.int.rB.rFPsc.v3.0anno
[1] 25210

$leaf.trt5E_live.DEGs.add.rB.rFPsc.v3.0anno
[1] 25210

$leaf.trt5E_live.DEGs.add.rB.rR500.v3.0anno
[1] 25210

$leaf.trt5E_live.DEGs.add.rD.rFPsc.v3.0anno
[1] 25210

$leaf.trt5E_live.DEGs.add.rD.rR500.v3.0anno
[1] 25210

$leaf.trt5E_live.genotypeFPsc_trt5E_live.DEGs.int.rB.rR500.v3.0anno
[1] 25210

$leaf.trt5E_live.genotypeFPsc_trt5E_live.DEGs.int.rD.rR500.v3.0anno
[1] 25210

$leaf.trt5E_live.genotypeFPsc.DEGs.int.rB.rR500.v3.0anno
[1] 25210

$leaf.trt5E_live.genotypeFPsc.DEGs.int.rD.rR500.v3.0anno
[1] 25210

$leaf.trt5E_live.genotypeR500_trt5E_live.DEGs.int.rB.rFPsc.v3.0anno
[1] 25210

$leaf.trt5E_live.genotypeR500_trt5E_live.DEGs.int.rD.rFPsc.v3.0anno
[1] 25210

$leaf.trt5E_live.genotypeR500.DEGs.int.rB.rFPsc.v3.0anno
[1] 25210

$root.FPsc.trtlive.DEGs.all.rD.v3.0anno
[1] 26380

$root.genotypeFPsc_trt5E_live.genotypeFPsc_trt5E_dead.genotypeFPsc.DEGs.int.rB.rR500.v3.0anno
[1] 27887

$root.genotypeFPsc_trt5E_live.genotypeFPsc_trtBLANK_NA.genotypeFPsc.DEGs.int.rD.rR500.v3.0anno
[1] 27887

$root.genotypeFPsc.DEGs.add.rB.rR500.v3.0anno
[1] 27887

$root.genotypeFPsc.DEGs.add.rD.rR500.v3.0anno
[1] 27887

$root.genotypeR500_trt5E_live.genotypeR500_trt5E_dead.genotypeR500.DEGs.int.rB.rFPsc.v3.0anno
[1] 27887

$root.genotypeR500_trt5E_live.genotypeR500_trtBLANK_NA.genotypeR500.DEGs.int.rD.rFPsc.v3.0anno
[1] 27887

$root.genotypeR500.DEGs.add.rB.rFPsc.v3.0anno
[1] 27887

$root.genotypeR500.DEGs.add.rD.rFPsc.v3.0anno
[1] 27887

$root.R500.trtlive.DEGs.all.rD.v3.0anno
[1] 26690

$root.trt5E_dead.DEGs.add.rB.rFPsc.v3.0anno
[1] 27887

$root.trt5E_dead.DEGs.add.rB.rR500.v3.0anno
[1] 27887

$root.trt5E_dead.genotypeFPsc_trt5E_dead.DEGs.int.rB.rR500.v3.0anno
[1] 27887

$root.trt5E_dead.genotypeR500_trt5E_dead.DEGs.int.rB.rFPsc.v3.0anno
[1] 27887

$root.trt5E_live.DEGs.add.rB.rFPsc.v3.0anno
[1] 27887

$root.trt5E_live.DEGs.add.rB.rR500.v3.0anno
[1] 27887

$root.trt5E_live.DEGs.add.rD.rFPsc.v3.0anno
[1] 27887

$root.trt5E_live.DEGs.add.rD.rR500.v3.0anno
[1] 27887

$root.trt5E_live.genotypeFPsc_trt5E_live.DEGs.int.rB.rR500.v3.0anno
[1] 27887

$root.trt5E_live.genotypeFPsc_trt5E_live.DEGs.int.rD.rR500.v3.0anno
[1] 27887

$root.trt5E_live.genotypeFPsc.DEGs.int.rB.rR500.v3.0anno
[1] 27887

$root.trt5E_live.genotypeFPsc.DEGs.int.rD.rR500.v3.0anno
[1] 27887

$root.trt5E_live.genotypeR500_trt5E_live.DEGs.int.rB.rFPsc.v3.0anno
[1] 27887

$root.trt5E_live.genotypeR500_trt5E_live.DEGs.int.rD.rFPsc.v3.0anno
[1] 27887

$root.trt5E_live.genotypeR500.DEGs.int.rB.rFPsc.v3.0anno
[1] 27887
map(DEG.count.list.e1.v3.0annotation.all,~filter(.x,FDR<0.05)) # does work
$leaf.FPsc.trtlive.DEGs.all.rD.v3.0anno
# A tibble: 2 x 11
     X1 genes logFC logCPM    LR  PValue     FDR AGI   At_symbol
  <int> <chr> <dbl>  <dbl> <dbl>   <dbl>   <dbl> <chr> <chr>    
1     1 BraA…  2.06  0.119  28.2 1.10e-7 0.00256 AT3G… <NA>     
2     2 BraA…  2.44  0.460  24.1 9.03e-7 0.0105  AT1G… AtVTL1   
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>

$leaf.genotypeFPsc_trt5E_live.genotypeFPsc_trt5E_dead.genotypeFPsc.DEGs.int.rB.rR500.v3.0anno
# A tibble: 18,895 x 13
      X1 genes logFC.genotypeF… logFC.genotypeF… logFC.genotypeF… logCPM
   <int> <chr>            <dbl>            <dbl>            <dbl>  <dbl>
 1     1 BraA…            -13.1           1.28             1.76     6.28
 2     2 BraA…            -12.4           0.829            0.0153   6.99
 3     3 BraA…             12.1          -0.791            1.16     6.40
 4     4 BraA…            -12.1          -0.0737           0.114    5.28
 5     5 BraA…            -12.1          -0.201           -0.825    6.50
 6     6 BraA…            -12.0           1.20            -0.163    5.28
 7     7 BraA…            -11.8           2.08             2.81     4.84
 8     8 BraA…             11.7          -1.18            -0.702    6.97
 9     9 BraA…            -11.7          -0.149           -0.115    4.94
10    10 BraA…            -11.6           0.0524           0.0330   4.78
# ... with 18,885 more rows, and 7 more variables: LR <dbl>, PValue <dbl>,
#   FDR <dbl>, AGI <chr>, At_symbol <chr>, At_short_description <chr>,
#   perc_ID <dbl>

$leaf.genotypeFPsc_trt5E_live.genotypeFPsc_trtBLANK_NA.genotypeFPsc.DEGs.int.rD.rR500.v3.0anno
# A tibble: 18,895 x 13
      X1 genes logFC.genotypeF… logFC.genotypeF… logFC.genotypeF… logCPM
   <int> <chr>            <dbl>            <dbl>            <dbl>  <dbl>
 1     1 BraA…            -13.3           2.23             3.29     6.34
 2     2 BraA…             12.8          -1.76            -1.60     5.99
 3     3 BraA…            -12.3           0.201           -0.624    6.50
 4     4 BraA…            -12.2           0.0737           0.188    5.28
 5     5 BraA…             12.1          -1.17            -1.38     5.13
 6     6 BraA…            -11.9           1.27             1.98     5.04
 7     7 BraA…            -11.8           0.149            0.0341   4.94
 8     8 BraA…            -11.8          -1.28             0.481    6.28
 9     9 BraA…            -11.6          -0.0524          -0.0194   4.78
10    10 BraA…            -11.5          -0.829           -0.814    6.99
# ... with 18,885 more rows, and 7 more variables: LR <dbl>, PValue <dbl>,
#   FDR <dbl>, AGI <chr>, At_symbol <chr>, At_short_description <chr>,
#   perc_ID <dbl>

$leaf.genotypeFPsc.DEGs.add.rB.rR500.v3.0anno
# A tibble: 19,658 x 11
      X1 genes logFC logCPM    LR PValue   FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>  <dbl> <dbl> <chr> <chr>    
 1     1 BraA… -12.4   6.50 2505.      0     0 AT1G… TAR4     
 2     2 BraA… -12.1   5.28 4344.      0     0 <NA>  <NA>     
 3     3 BraA…  12.1   6.40 3411.      0     0 AT2G… ATCNGC11 
 4     4 BraA… -12.1   6.99 1955.      0     0 AT4G… CRK39    
 5     5 BraA… -11.9   6.28 1578.      0     0 AT1G… ATBBD1   
 6     6 BraA… -11.8   4.94 1986.      0     0 <NA>  <NA>     
 7     7 BraA… -11.6   4.78 3000.      0     0 <NA>  <NA>     
 8     8 BraA… -11.6   5.28 3458.      0     0 AT1G… <NA>     
 9     9 BraA… -11.5   4.63 2430.      0     0 AT5G… <NA>     
10    10 BraA…  11.4   5.99 5024.      0     0 <NA>  <NA>     
# ... with 19,648 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$leaf.genotypeFPsc.DEGs.add.rD.rR500.v3.0anno
# A tibble: 19,658 x 11
      X1 genes logFC logCPM    LR PValue   FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>  <dbl> <dbl> <chr> <chr>    
 1     1 BraA… -12.4   6.50 2505.      0     0 AT1G… TAR4     
 2     2 BraA… -12.1   5.28 4344.      0     0 <NA>  <NA>     
 3     3 BraA…  12.1   6.40 3411.      0     0 AT2G… ATCNGC11 
 4     4 BraA… -12.1   6.99 1955.      0     0 AT4G… CRK39    
 5     5 BraA… -11.9   6.28 1578.      0     0 AT1G… ATBBD1   
 6     6 BraA… -11.8   4.94 1986.      0     0 <NA>  <NA>     
 7     7 BraA… -11.6   4.78 3000.      0     0 <NA>  <NA>     
 8     8 BraA… -11.6   5.28 3458.      0     0 AT1G… <NA>     
 9     9 BraA… -11.5   4.63 2430.      0     0 AT5G… <NA>     
10    10 BraA…  11.4   5.99 5024.      0     0 <NA>  <NA>     
# ... with 19,648 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$leaf.genotypeR500_trt5E_live.genotypeR500_trt5E_dead.genotypeR500.DEGs.int.rB.rFPsc.v3.0anno
# A tibble: 18,895 x 13
      X1 genes logFC.genotypeR… logFC.genotypeR… logFC.genotypeR… logCPM
   <int> <chr>            <dbl>            <dbl>            <dbl>  <dbl>
 1     1 BraA…             13.1          -1.28            -1.76     6.28
 2     2 BraA…             12.4          -0.829           -0.0153   6.99
 3     3 BraA…            -12.1           0.791           -1.16     6.40
 4     4 BraA…             12.1           0.0737          -0.114    5.28
 5     5 BraA…             12.1           0.201            0.825    6.50
 6     6 BraA…             12.0          -1.20             0.163    5.28
 7     7 BraA…             11.8          -2.08            -2.81     4.84
 8     8 BraA…            -11.7           1.18             0.702    6.97
 9     9 BraA…             11.7           0.149            0.115    4.94
10    10 BraA…             11.6          -0.0524          -0.0330   4.78
# ... with 18,885 more rows, and 7 more variables: LR <dbl>, PValue <dbl>,
#   FDR <dbl>, AGI <chr>, At_symbol <chr>, At_short_description <chr>,
#   perc_ID <dbl>

$leaf.genotypeR500_trt5E_live.genotypeR500_trtBLANK_NA.genotypeR500.DEGs.int.rD.rFPsc.v3.0anno
# A tibble: 18,895 x 13
      X1 genes logFC.genotypeR… logFC.genotypeR… logFC.genotypeR… logCPM
   <int> <chr>            <dbl>            <dbl>            <dbl>  <dbl>
 1     1 BraA…             13.3          -2.23            -3.29     6.34
 2     2 BraA…            -12.8           1.76             1.60     5.99
 3     3 BraA…             12.3          -0.201            0.624    6.50
 4     4 BraA…             12.2          -0.0737          -0.188    5.28
 5     5 BraA…            -12.1           1.17             1.38     5.13
 6     6 BraA…             11.9          -1.27            -1.98     5.04
 7     7 BraA…             11.8          -0.149           -0.0341   4.94
 8     8 BraA…             11.8           1.28            -0.481    6.28
 9     9 BraA…             11.6           0.0524           0.0194   4.78
10    10 BraA…             11.5           0.829            0.814    6.99
# ... with 18,885 more rows, and 7 more variables: LR <dbl>, PValue <dbl>,
#   FDR <dbl>, AGI <chr>, At_symbol <chr>, At_short_description <chr>,
#   perc_ID <dbl>

$leaf.genotypeR500.DEGs.add.rB.rFPsc.v3.0anno
# A tibble: 19,658 x 11
      X1 genes logFC logCPM    LR PValue   FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>  <dbl> <dbl> <chr> <chr>    
 1     1 BraA…  12.4   6.50 2505.      0     0 AT1G… TAR4     
 2     2 BraA…  12.1   5.28 4344.      0     0 <NA>  <NA>     
 3     3 BraA… -12.1   6.40 3411.      0     0 AT2G… ATCNGC11 
 4     4 BraA…  12.1   6.99 1955.      0     0 AT4G… CRK39    
 5     5 BraA…  11.9   6.28 1578.      0     0 AT1G… ATBBD1   
 6     6 BraA…  11.8   4.94 1986.      0     0 <NA>  <NA>     
 7     7 BraA…  11.6   4.78 3000.      0     0 <NA>  <NA>     
 8     8 BraA…  11.6   5.28 3458.      0     0 AT1G… <NA>     
 9     9 BraA…  11.5   4.63 2430.      0     0 AT5G… <NA>     
10    10 BraA… -11.4   5.99 5024.      0     0 <NA>  <NA>     
# ... with 19,648 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$leaf.genotypeR500.DEGs.add.rD.rFPsc.v3.0anno
# A tibble: 19,658 x 11
      X1 genes logFC logCPM    LR PValue   FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>  <dbl> <dbl> <chr> <chr>    
 1     1 BraA…  12.4   6.50 2505.      0     0 AT1G… TAR4     
 2     2 BraA…  12.1   5.28 4344.      0     0 <NA>  <NA>     
 3     3 BraA… -12.1   6.40 3411.      0     0 AT2G… ATCNGC11 
 4     4 BraA…  12.1   6.99 1955.      0     0 AT4G… CRK39    
 5     5 BraA…  11.9   6.28 1578.      0     0 AT1G… ATBBD1   
 6     6 BraA…  11.8   4.94 1986.      0     0 <NA>  <NA>     
 7     7 BraA…  11.6   4.78 3000.      0     0 <NA>  <NA>     
 8     8 BraA…  11.6   5.28 3458.      0     0 AT1G… <NA>     
 9     9 BraA…  11.5   4.63 2430.      0     0 AT5G… <NA>     
10    10 BraA… -11.4   5.99 5024.      0     0 <NA>  <NA>     
# ... with 19,648 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$leaf.R500.trtlive.DEGs.all.rD.v3.0anno
# A tibble: 1,927 x 11
      X1 genes logFC logCPM    LR   PValue      FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>    <dbl>    <dbl> <chr> <chr>    
 1     1 BraA… -2.06   5.13  64.4 9.98e-16 2.40e-11 AT2G… ATP5CS   
 2     2 BraA… -1.55   5.25  42.0 9.02e-11 1.09e- 6 AT5G… AtcPT4   
 3     3 BraA… -1.67   2.22  37.2 1.04e- 9 8.35e- 6 AT1G… ATGSTU25 
 4     4 BraA… -1.18   3.93  36.1 1.86e- 9 1.12e- 5 AT2G… ANNAT4   
 5     5 BraA… -2.08   1.98  35.7 2.33e- 9 1.12e- 5 AT5G… <NA>     
 6     6 BraA…  2.53   3.65  34.3 4.63e- 9 1.86e- 5 AT3G… CYP72A8  
 7     7 BraA… -1.63   1.89  33.7 6.36e- 9 2.19e- 5 AT5G… <NA>     
 8     8 BraA… -1.94   7.40  32.9 9.50e- 9 2.86e- 5 AT3G… UGP3     
 9     9 BraA… -2.93   2.43  32.6 1.10e- 8 2.95e- 5 AT1G… AtPFA-DS…
10    10 BraA… -2.27   6.82  32.4 1.24e- 8 2.99e- 5 AT1G… ATPPCK1  
# ... with 1,917 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$leaf.trt5E_dead.DEGs.add.rB.rFPsc.v3.0anno
# A tibble: 0 x 11
# ... with 11 variables: X1 <int>, genes <chr>, logFC <dbl>, logCPM <dbl>,
#   LR <dbl>, PValue <dbl>, FDR <dbl>, AGI <chr>, At_symbol <chr>,
#   At_short_description <chr>, perc_ID <dbl>

$leaf.trt5E_dead.DEGs.add.rB.rR500.v3.0anno
# A tibble: 0 x 11
# ... with 11 variables: X1 <int>, genes <chr>, logFC <dbl>, logCPM <dbl>,
#   LR <dbl>, PValue <dbl>, FDR <dbl>, AGI <chr>, At_symbol <chr>,
#   At_short_description <chr>, perc_ID <dbl>

$leaf.trt5E_dead.genotypeFPsc_trt5E_dead.DEGs.int.rB.rR500.v3.0anno
# A tibble: 2 x 12
     X1 genes logFC.trt5E_dead logFC.genotypeF… logCPM    LR  PValue
  <int> <chr>            <dbl>            <dbl>  <dbl> <dbl>   <dbl>
1     1 BraA…             1.31            -1.19   4.33  30.4 2.49e-7
2     2 BraA…             5.60            -5.46   3.93  30.4 2.56e-7
# ... with 5 more variables: FDR <dbl>, AGI <chr>, At_symbol <chr>,
#   At_short_description <chr>, perc_ID <dbl>

$leaf.trt5E_dead.genotypeR500_trt5E_dead.DEGs.int.rB.rFPsc.v3.0anno
# A tibble: 2 x 12
     X1 genes logFC.trt5E_dead logFC.genotypeR… logCPM    LR  PValue
  <int> <chr>            <dbl>            <dbl>  <dbl> <dbl>   <dbl>
1     1 BraA…            0.124             1.19   4.33  30.4 2.49e-7
2     2 BraA…            0.142             5.46   3.93  30.4 2.56e-7
# ... with 5 more variables: FDR <dbl>, AGI <chr>, At_symbol <chr>,
#   At_short_description <chr>, perc_ID <dbl>

$leaf.trt5E_live.DEGs.add.rB.rFPsc.v3.0anno
# A tibble: 144 x 11
      X1 genes  logFC logCPM    LR  PValue     FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>   <dbl>   <dbl> <chr> <chr>    
 1     1 BraA…  0.617  3.31   29.9 4.54e-8 0.00114 AT1G… <NA>     
 2     2 BraA… -1.74   3.55   28.1 1.16e-7 0.00146 AT1G… AtWSCP   
 3     3 BraA…  0.579  3.07   24.4 7.75e-7 0.00619 AT5G… ATHIR1   
 4     4 BraA… -1.30   0.169  24.0 9.82e-7 0.00619 AT1G… GXM1     
 5     5 BraA… -0.573  5.72   22.0 2.77e-6 0.00936 AT1G… ADT1     
 6     6 BraA… -0.625  3.09   21.9 2.82e-6 0.00936 AT4G… GrxC5    
 7     7 BraA… -0.615  3.75   21.7 3.13e-6 0.00936 AT2G… ALF1     
 8     8 BraA… -1.63   2.99   21.7 3.26e-6 0.00936 AT1G… <NA>     
 9     9 BraA…  1.52  -0.158  21.6 3.34e-6 0.00936 AT4G… ATK5     
10    10 BraA… -0.550  3.01   20.9 4.91e-6 0.0124  AT5G… <NA>     
# ... with 134 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$leaf.trt5E_live.DEGs.add.rB.rR500.v3.0anno
# A tibble: 144 x 11
      X1 genes  logFC logCPM    LR  PValue     FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>   <dbl>   <dbl> <chr> <chr>    
 1     1 BraA…  0.617  3.31   29.9 4.54e-8 0.00114 AT1G… <NA>     
 2     2 BraA… -1.74   3.55   28.1 1.16e-7 0.00146 AT1G… AtWSCP   
 3     3 BraA…  0.579  3.07   24.4 7.75e-7 0.00619 AT5G… ATHIR1   
 4     4 BraA… -1.30   0.169  24.0 9.82e-7 0.00619 AT1G… GXM1     
 5     5 BraA… -0.573  5.72   22.0 2.77e-6 0.00936 AT1G… ADT1     
 6     6 BraA… -0.625  3.09   21.9 2.82e-6 0.00936 AT4G… GrxC5    
 7     7 BraA… -0.615  3.75   21.7 3.13e-6 0.00936 AT2G… ALF1     
 8     8 BraA… -1.63   2.99   21.7 3.26e-6 0.00936 AT1G… <NA>     
 9     9 BraA…  1.52  -0.158  21.6 3.34e-6 0.00936 AT4G… ATK5     
10    10 BraA… -0.550  3.01   20.9 4.91e-6 0.0124  AT5G… <NA>     
# ... with 134 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$leaf.trt5E_live.DEGs.add.rD.rFPsc.v3.0anno
# A tibble: 1,932 x 11
      X1 genes  logFC logCPM    LR   PValue     FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>    <dbl>   <dbl> <chr> <chr>    
 1     1 BraA… -1.63   1.26   38.1 6.58e-10 1.66e-5 AT1G… ATGSTU25 
 2     2 BraA… -1.88   3.55   32.3 1.29e- 8 1.44e-4 AT1G… AtWSCP   
 3     3 BraA… -0.737  3.75   31.1 2.45e- 8 1.44e-4 AT2G… ALF1     
 4     4 BraA…  1.25   0.725  31.0 2.56e- 8 1.44e-4 <NA>  <NA>     
 5     5 BraA…  0.889  5.15   30.8 2.85e- 8 1.44e-4 AT5G… <NA>     
 6     6 BraA…  0.841  3.81   30.2 3.85e- 8 1.62e-4 AT5G… <NA>     
 7     7 BraA…  1.44   1.69   29.8 4.91e- 8 1.77e-4 AT1G… SMR2     
 8     8 BraA…  1.80   1.28   27.9 1.26e- 7 3.96e-4 AT3G… <NA>     
 9     9 BraA…  0.537  3.28   27.6 1.51e- 7 4.22e-4 AT5G… ATFIP1[V]
10    10 BraA… -0.370  5.90   26.9 2.18e- 7 5.36e-4 AT1G… ARC12    
# ... with 1,922 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$leaf.trt5E_live.DEGs.add.rD.rR500.v3.0anno
# A tibble: 1,932 x 11
      X1 genes  logFC logCPM    LR   PValue     FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>    <dbl>   <dbl> <chr> <chr>    
 1     1 BraA… -1.63   1.26   38.1 6.58e-10 1.66e-5 AT1G… ATGSTU25 
 2     2 BraA… -1.88   3.55   32.3 1.29e- 8 1.44e-4 AT1G… AtWSCP   
 3     3 BraA… -0.737  3.75   31.1 2.45e- 8 1.44e-4 AT2G… ALF1     
 4     4 BraA…  1.25   0.725  31.0 2.56e- 8 1.44e-4 <NA>  <NA>     
 5     5 BraA…  0.889  5.15   30.8 2.85e- 8 1.44e-4 AT5G… <NA>     
 6     6 BraA…  0.841  3.81   30.2 3.85e- 8 1.62e-4 AT5G… <NA>     
 7     7 BraA…  1.44   1.69   29.8 4.91e- 8 1.77e-4 AT1G… SMR2     
 8     8 BraA…  1.80   1.28   27.9 1.26e- 7 3.96e-4 AT3G… <NA>     
 9     9 BraA…  0.537  3.28   27.6 1.51e- 7 4.22e-4 AT5G… ATFIP1[V]
10    10 BraA… -0.370  5.90   26.9 2.18e- 7 5.36e-4 AT1G… ARC12    
# ... with 1,922 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$leaf.trt5E_live.genotypeFPsc_trt5E_live.DEGs.int.rB.rR500.v3.0anno
# A tibble: 399 x 12
      X1 genes logFC.trt5E_live logFC.genotypeF… logCPM    LR   PValue
   <int> <chr>            <dbl>            <dbl>  <dbl> <dbl>    <dbl>
 1     1 BraA…           -1.44             1.44    3.15  45.2 1.53e-10
 2     2 BraA…           -0.107            4.00    1.98  37.2 8.22e- 9
 3     3 BraA…            0.503            0.261   3.31  31.4 1.53e- 7
 4     4 BraA…           -5.55             4.85    6.89  30.8 2.02e- 7
 5     5 BraA…           -2.03             2.06    3.23  30.4 2.55e- 7
 6     6 BraA…           -0.842            0.719   7.36  29.9 3.24e- 7
 7     7 BraA…           -1.26             1.05    4.67  29.8 3.32e- 7
 8     8 BraA…           -1.73             1.82    2.32  29.7 3.54e- 7
 9     9 BraA…            5.51            -5.39    3.93  29.1 4.72e- 7
10    10 BraA…           -1.77             1.82    3.55  28.3 7.33e- 7
# ... with 389 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$leaf.trt5E_live.genotypeFPsc_trt5E_live.DEGs.int.rD.rR500.v3.0anno
# A tibble: 2,061 x 12
      X1 genes logFC.trt5E_live logFC.genotypeF… logCPM    LR   PValue
   <int> <chr>            <dbl>            <dbl>  <dbl> <dbl>    <dbl>
 1     1 BraA…            -2.05            2.10    4.33  69.8 6.82e-16
 2     2 BraA…            -2.93            2.85    2.99  50.6 1.05e-11
 3     3 BraA…             1.36           -1.10    4.25  45.3 1.44e-10
 4     4 BraA…            -2.25            1.85    7.95  44.9 1.77e-10
 5     5 BraA…            -1.06            0.665   3.75  44.7 1.94e-10
 6     6 BraA…            -2.43            1.96    3.99  42.5 5.87e-10
 7     7 BraA…             2.36           -2.08    3.32  40.7 1.48e- 9
 8     8 BraA…             1.22           -0.692   5.15  38.5 4.34e- 9
 9     9 BraA…            -1.67            1.09    1.26  38.2 4.98e- 9
10    10 BraA…            -4.17            3.88    3.53  37.6 6.82e- 9
# ... with 2,051 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$leaf.trt5E_live.genotypeFPsc.DEGs.int.rB.rR500.v3.0anno
# A tibble: 5 x 11
     X1 genes logFC logCPM    LR  PValue     FDR AGI   At_symbol
  <int> <chr> <dbl>  <dbl> <dbl>   <dbl>   <dbl> <chr> <chr>    
1     1 BraA…  4.00   1.98  34.5 4.19e-9 1.06e-4 <NA>  <NA>     
2     2 BraA… -5.39   3.93  21.6 3.33e-6 2.89e-2 AT1G… ATU2AF65B
3     3 BraA…  1.44   3.15  21.6 3.43e-6 2.89e-2 AT1G… ASB1     
4     4 BraA… -4.43   2.62  20.2 7.13e-6 4.50e-2 AT2G… ATPEX10  
5     5 BraA…  2.41   2.99  19.6 9.72e-6 4.90e-2 AT1G… AtPFA-DS…
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>

$leaf.trt5E_live.genotypeFPsc.DEGs.int.rD.rR500.v3.0anno
# A tibble: 8 x 11
     X1 genes logFC logCPM    LR   PValue     FDR AGI   At_symbol
  <int> <chr> <dbl>  <dbl> <dbl>    <dbl>   <dbl> <chr> <chr>    
1     1 BraA…  2.10   4.33  35.4  2.65e-9 6.68e-5 AT2G… ATP5CS   
2     2 BraA…  3.21   2.98  31.8  1.72e-8 2.17e-4 AT5G… ABCF2    
3     3 BraA…  2.85   2.99  27.7  1.43e-7 1.20e-3 AT1G… AtPFA-DS…
4     4 BraA…  1.72   5.63  22.7  1.91e-6 1.20e-2 AT5G… AtcPT4   
5     5 BraA… -3.46   2.58  21.0  4.51e-6 2.27e-2 AT1G… ATGPT2   
6     6 BraA…  3.88   3.53  19.8  8.40e-6 3.53e-2 AT3G… ATACP5   
7     7 BraA… -2.08   3.32  19.5 10.00e-6 3.60e-2 AT5G… <NA>     
8     8 BraA…  2.81   1.29  19.0  1.31e-5 4.14e-2 AT5G… <NA>     
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>

$leaf.trt5E_live.genotypeR500_trt5E_live.DEGs.int.rB.rFPsc.v3.0anno
# A tibble: 399 x 12
      X1 genes logFC.trt5E_live logFC.genotypeR… logCPM    LR   PValue
   <int> <chr>            <dbl>            <dbl>  <dbl> <dbl>    <dbl>
 1     1 BraA…          0.00152           -1.44    3.15  45.2 1.53e-10
 2     2 BraA…          3.89              -4.00    1.98  37.2 8.22e- 9
 3     3 BraA…          0.764             -0.261   3.31  31.4 1.53e- 7
 4     4 BraA…         -0.695             -4.85    6.89  30.8 2.02e- 7
 5     5 BraA…          0.0355            -2.06    3.23  30.4 2.55e- 7
 6     6 BraA…         -0.123             -0.719   7.36  29.9 3.24e- 7
 7     7 BraA…         -0.209             -1.05    4.67  29.8 3.32e- 7
 8     8 BraA…          0.0889            -1.82    2.32  29.7 3.54e- 7
 9     9 BraA…          0.117              5.39    3.93  29.1 4.72e- 7
10    10 BraA…          0.0435            -1.82    3.55  28.3 7.33e- 7
# ... with 389 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$leaf.trt5E_live.genotypeR500_trt5E_live.DEGs.int.rD.rFPsc.v3.0anno
# A tibble: 2,061 x 12
      X1 genes logFC.trt5E_live logFC.genotypeR… logCPM    LR   PValue
   <int> <chr>            <dbl>            <dbl>  <dbl> <dbl>    <dbl>
 1     1 BraA…           0.0565           -2.10    4.33  69.8 6.82e-16
 2     2 BraA…          -0.0794           -2.85    2.99  50.6 1.05e-11
 3     3 BraA…           0.263             1.10    4.25  45.3 1.44e-10
 4     4 BraA…          -0.407            -1.85    7.95  44.9 1.77e-10
 5     5 BraA…          -0.393            -0.665   3.75  44.7 1.94e-10
 6     6 BraA…          -0.471            -1.96    3.99  42.5 5.87e-10
 7     7 BraA…           0.286             2.08    3.32  40.7 1.48e- 9
 8     8 BraA…           0.523             0.692   5.15  38.5 4.34e- 9
 9     9 BraA…          -0.583            -1.09    1.26  38.2 4.98e- 9
10    10 BraA…          -0.288            -3.88    3.53  37.6 6.82e- 9
# ... with 2,051 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$leaf.trt5E_live.genotypeR500.DEGs.int.rB.rFPsc.v3.0anno
# A tibble: 5 x 11
     X1 genes logFC logCPM    LR  PValue     FDR AGI   At_symbol
  <int> <chr> <dbl>  <dbl> <dbl>   <dbl>   <dbl> <chr> <chr>    
1     1 BraA… -4.00   1.98  34.5 4.19e-9 1.06e-4 <NA>  <NA>     
2     2 BraA…  5.39   3.93  21.6 3.33e-6 2.89e-2 AT1G… ATU2AF65B
3     3 BraA… -1.44   3.15  21.6 3.43e-6 2.89e-2 AT1G… ASB1     
4     4 BraA…  4.43   2.62  20.2 7.13e-6 4.50e-2 AT2G… ATPEX10  
5     5 BraA… -2.41   2.99  19.6 9.72e-6 4.90e-2 AT1G… AtPFA-DS…
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>

$root.FPsc.trtlive.DEGs.all.rD.v3.0anno
# A tibble: 9 x 11
     X1 genes  logFC logCPM    LR   PValue     FDR AGI   At_symbol
  <int> <chr>  <dbl>  <dbl> <dbl>    <dbl>   <dbl> <chr> <chr>    
1     1 BraA… -1.70   5.74   37.9 7.54e-10 1.99e-5 AT1G… <NA>     
2     2 BraA… -2.70   0.746  27.1 1.92e- 7 2.53e-3 AT5G… CGLD27   
3     3 BraA…  4.90   4.78   24.9 6.18e- 7 5.43e-3 AT5G… HSP18.2  
4     4 BraA…  3.02   4.43   21.3 3.97e- 6 2.27e-2 AT5G… HSP18.2  
5     5 BraA… -1.05   7.43   21.1 4.30e- 6 2.27e-2 AT1G… ATOPR2   
6     6 BraA… -0.761  2.51   20.6 5.79e- 6 2.43e-2 AT1G… <NA>     
7     7 BraA…  2.53   0.780  20.3 6.46e- 6 2.43e-2 AT3G… <NA>     
8     8 BraA… -1.31   3.16   19.5 9.87e- 6 2.96e-2 AT3G… BHLH039  
9     9 BraA… -0.938  6.99   19.5 1.01e- 5 2.96e-2 AT3G… AtDJ1A   
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>

$root.genotypeFPsc_trt5E_live.genotypeFPsc_trt5E_dead.genotypeFPsc.DEGs.int.rB.rR500.v3.0anno
# A tibble: 17,373 x 13
      X1 genes logFC.genotypeF… logFC.genotypeF… logFC.genotypeF… logCPM
   <int> <chr>            <dbl>            <dbl>            <dbl>  <dbl>
 1     1 BraA…             14.4          -2.48            -2.08     7.57
 2     2 BraA…            -14.3           1.08             1.42     7.50
 3     3 BraA…             13.6          -1.30            -0.0224   6.77
 4     4 BraA…             13.0          -1.33            -1.99     6.18
 5     5 BraA…            -12.6           2.16             2.96     5.81
 6     6 BraA…             12.5          -4.21            -4.13     5.83
 7     7 BraA…             12.3          -0.131           -1.29     5.50
 8     8 BraA…             12.3          -1.42            -0.269    5.36
 9     9 BraA…             12.2           0.0831          -1.14     5.49
10    10 BraA…             12.1          -0.139           -2.13     5.21
# ... with 17,363 more rows, and 7 more variables: LR <dbl>, PValue <dbl>,
#   FDR <dbl>, AGI <chr>, At_symbol <chr>, At_short_description <chr>,
#   perc_ID <dbl>

$root.genotypeFPsc_trt5E_live.genotypeFPsc_trtBLANK_NA.genotypeFPsc.DEGs.int.rD.rR500.v3.0anno
# A tibble: 17,373 x 13
      X1 genes logFC.genotypeF… logFC.genotypeF… logFC.genotypeF… logCPM
   <int> <chr>            <dbl>            <dbl>            <dbl>  <dbl>
 1     1 BraA…             13.3          -1.28             0.0181   6.55
 2     2 BraA…            -13.2          -1.08             0.338    7.50
 3     3 BraA…            -13.2           1.76             1.23     6.43
 4     4 BraA…            -12.5           0.465            1.32     7.08
 5     5 BraA…             12.3          -0.0831          -1.22     5.49
 6     6 BraA…             12.2           1.30             1.28     6.77
 7     7 BraA…             12.2           0.131           -1.16     5.50
 8     8 BraA…            -12.0           1.24             1.70     5.33
 9     9 BraA…             12.0           0.139           -1.99     5.21
10    10 BraA…             11.9           2.48             0.395    7.57
# ... with 17,363 more rows, and 7 more variables: LR <dbl>, PValue <dbl>,
#   FDR <dbl>, AGI <chr>, At_symbol <chr>, At_short_description <chr>,
#   perc_ID <dbl>

$root.genotypeFPsc.DEGs.add.rB.rR500.v3.0anno
# A tibble: 18,989 x 11
      X1 genes logFC logCPM    LR PValue   FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>  <dbl> <dbl> <chr> <chr>    
 1     1 BraA… -13.4   7.50 3038.      0     0 AT1G… <NA>     
 2     2 BraA…  13.0   6.77 1714.      0     0 <NA>  <NA>     
 3     3 BraA…  12.8   6.55 5105.      0     0 <NA>  <NA>     
 4     4 BraA…  12.6   7.57 2909.      0     0 AT2G… <NA>     
 5     5 BraA… -12.0   6.43 5449.      0     0 <NA>  <NA>     
 6     6 BraA… -11.8   7.08 3622.      0     0 AT3G… <NA>     
 7     7 BraA…  11.7   5.50 3920.      0     0 <NA>  <NA>     
 8     8 BraA…  11.7   5.49 3480.      0     0 <NA>  <NA>     
 9     9 BraA…  11.7   6.18 3861.      0     0 AT5G… <NA>     
10    10 BraA…  11.6   5.36 2391.      0     0 <NA>  <NA>     
# ... with 18,979 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.genotypeFPsc.DEGs.add.rD.rR500.v3.0anno
# A tibble: 18,989 x 11
      X1 genes logFC logCPM    LR PValue   FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>  <dbl> <dbl> <chr> <chr>    
 1     1 BraA… -13.4   7.50 3038.      0     0 AT1G… <NA>     
 2     2 BraA…  13.0   6.77 1714.      0     0 <NA>  <NA>     
 3     3 BraA…  12.8   6.55 5105.      0     0 <NA>  <NA>     
 4     4 BraA…  12.6   7.57 2909.      0     0 AT2G… <NA>     
 5     5 BraA… -12.0   6.43 5449.      0     0 <NA>  <NA>     
 6     6 BraA… -11.8   7.08 3622.      0     0 AT3G… <NA>     
 7     7 BraA…  11.7   5.50 3920.      0     0 <NA>  <NA>     
 8     8 BraA…  11.7   5.49 3480.      0     0 <NA>  <NA>     
 9     9 BraA…  11.7   6.18 3861.      0     0 AT5G… <NA>     
10    10 BraA…  11.6   5.36 2391.      0     0 <NA>  <NA>     
# ... with 18,979 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.genotypeR500_trt5E_live.genotypeR500_trt5E_dead.genotypeR500.DEGs.int.rB.rFPsc.v3.0anno
# A tibble: 17,373 x 13
      X1 genes logFC.genotypeR… logFC.genotypeR… logFC.genotypeR… logCPM
   <int> <chr>            <dbl>            <dbl>            <dbl>  <dbl>
 1     1 BraA…            -14.4           2.48             2.08     7.57
 2     2 BraA…             14.3          -1.08            -1.42     7.50
 3     3 BraA…            -13.6           1.30             0.0224   6.77
 4     4 BraA…            -13.0           1.33             1.99     6.18
 5     5 BraA…             12.6          -2.16            -2.96     5.81
 6     6 BraA…            -12.5           4.21             4.13     5.83
 7     7 BraA…            -12.3           0.131            1.29     5.50
 8     8 BraA…            -12.3           1.42             0.269    5.36
 9     9 BraA…            -12.2          -0.0831           1.14     5.49
10    10 BraA…            -12.1           0.139            2.13     5.21
# ... with 17,363 more rows, and 7 more variables: LR <dbl>, PValue <dbl>,
#   FDR <dbl>, AGI <chr>, At_symbol <chr>, At_short_description <chr>,
#   perc_ID <dbl>

$root.genotypeR500_trt5E_live.genotypeR500_trtBLANK_NA.genotypeR500.DEGs.int.rD.rFPsc.v3.0anno
# A tibble: 17,373 x 13
      X1 genes logFC.genotypeR… logFC.genotypeR… logFC.genotypeR… logCPM
   <int> <chr>            <dbl>            <dbl>            <dbl>  <dbl>
 1     1 BraA…            -13.3           1.28            -0.0181   6.55
 2     2 BraA…             13.2           1.08            -0.338    7.50
 3     3 BraA…             13.2          -1.76            -1.23     6.43
 4     4 BraA…             12.5          -0.465           -1.32     7.08
 5     5 BraA…            -12.3           0.0831           1.22     5.49
 6     6 BraA…            -12.2          -1.30            -1.28     6.77
 7     7 BraA…            -12.2          -0.131            1.16     5.50
 8     8 BraA…             12.0          -1.24            -1.70     5.33
 9     9 BraA…            -12.0          -0.139            1.99     5.21
10    10 BraA…            -11.9          -2.48            -0.395    7.57
# ... with 17,363 more rows, and 7 more variables: LR <dbl>, PValue <dbl>,
#   FDR <dbl>, AGI <chr>, At_symbol <chr>, At_short_description <chr>,
#   perc_ID <dbl>

$root.genotypeR500.DEGs.add.rB.rFPsc.v3.0anno
# A tibble: 18,989 x 11
      X1 genes logFC logCPM    LR PValue   FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>  <dbl> <dbl> <chr> <chr>    
 1     1 BraA…  13.4   7.50 3038.      0     0 AT1G… <NA>     
 2     2 BraA… -13.0   6.77 1714.      0     0 <NA>  <NA>     
 3     3 BraA… -12.8   6.55 5105.      0     0 <NA>  <NA>     
 4     4 BraA… -12.6   7.57 2909.      0     0 AT2G… <NA>     
 5     5 BraA…  12.0   6.43 5449.      0     0 <NA>  <NA>     
 6     6 BraA…  11.8   7.08 3622.      0     0 AT3G… <NA>     
 7     7 BraA… -11.7   5.50 3920.      0     0 <NA>  <NA>     
 8     8 BraA… -11.7   5.49 3480.      0     0 <NA>  <NA>     
 9     9 BraA… -11.7   6.18 3861.      0     0 AT5G… <NA>     
10    10 BraA… -11.6   5.36 2391.      0     0 <NA>  <NA>     
# ... with 18,979 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.genotypeR500.DEGs.add.rD.rFPsc.v3.0anno
# A tibble: 18,989 x 11
      X1 genes logFC logCPM    LR PValue   FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>  <dbl> <dbl> <chr> <chr>    
 1     1 BraA…  13.4   7.50 3038.      0     0 AT1G… <NA>     
 2     2 BraA… -13.0   6.77 1714.      0     0 <NA>  <NA>     
 3     3 BraA… -12.8   6.55 5105.      0     0 <NA>  <NA>     
 4     4 BraA… -12.6   7.57 2909.      0     0 AT2G… <NA>     
 5     5 BraA…  12.0   6.43 5449.      0     0 <NA>  <NA>     
 6     6 BraA…  11.8   7.08 3622.      0     0 AT3G… <NA>     
 7     7 BraA… -11.7   5.50 3920.      0     0 <NA>  <NA>     
 8     8 BraA… -11.7   5.49 3480.      0     0 <NA>  <NA>     
 9     9 BraA… -11.7   6.18 3861.      0     0 AT5G… <NA>     
10    10 BraA… -11.6   5.36 2391.      0     0 <NA>  <NA>     
# ... with 18,979 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.R500.trtlive.DEGs.all.rD.v3.0anno
# A tibble: 383 x 11
      X1 genes  logFC logCPM    LR  PValue     FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>   <dbl>   <dbl> <chr> <chr>    
 1     1 BraA…  1.26    4.60  33.9 5.82e-9 1.55e-4 AT1G… NLP4     
 2     2 BraA…  2.13    3.39  32.5 1.20e-8 1.60e-4 AT1G… <NA>     
 3     3 BraA…  2.23    1.67  31.4 2.05e-8 1.83e-4 AT3G… ABCA3    
 4     4 BraA…  1.70    3.81  30.6 3.14e-8 1.93e-4 AT3G… NF-YA6   
 5     5 BraA… -1.53    4.64  30.3 3.61e-8 1.93e-4 AT4G… <NA>     
 6     6 BraA…  1.28    3.98  29.2 6.42e-8 2.86e-4 AT5G… GLN1;4   
 7     7 BraA… -1.14    5.84  28.4 1.00e-7 3.29e-4 AT1G… AtNIGT1  
 8     8 BraA…  0.988   5.18  28.2 1.09e-7 3.29e-4 AT5G… <NA>     
 9     9 BraA…  1.77    5.64  28.2 1.12e-7 3.29e-4 AT5G… ATDUR3   
10    10 BraA… -1.37    3.74  27.9 1.30e-7 3.29e-4 AT1G… AtNIGT1  
# ... with 373 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.trt5E_dead.DEGs.add.rB.rFPsc.v3.0anno
# A tibble: 23 x 11
      X1 genes  logFC  logCPM    LR  PValue     FDR AGI   At_symbol
   <int> <chr>  <dbl>   <dbl> <dbl>   <dbl>   <dbl> <chr> <chr>    
 1     1 BraA…  1.42   2.28    32.0 1.53e-8 4.27e-4 AT5G… <NA>     
 2     2 BraA…  1.99   1.62    26.6 2.46e-7 3.43e-3 AT4G… CYP82C4  
 3     3 BraA…  0.941  2.67    24.2 8.86e-7 7.05e-3 AT3G… <NA>     
 4     4 BraA…  1.81   1.53    23.9 1.01e-6 7.05e-3 AT4G… ATIRT1   
 5     5 BraA…  1.67   0.0566  20.8 5.15e-6 2.73e-2 AT1G… <NA>     
 6     6 BraA…  1.43   0.469   20.5 5.87e-6 2.73e-2 AT2G… Iqd4     
 7     7 BraA…  1.42   2.16    19.9 8.24e-6 3.28e-2 AT2G… <NA>     
 8     8 BraA…  1.45   3.39    19.5 1.02e-5 3.28e-2 AT5G… <NA>     
 9     9 BraA…  1.47   2.36    19.2 1.16e-5 3.28e-2 AT5G… ATPT4    
10    10 BraA… -4.78  -0.507   19.1 1.26e-5 3.28e-2 <NA>  <NA>     
# ... with 13 more rows, and 2 more variables: At_short_description <chr>,
#   perc_ID <dbl>

$root.trt5E_dead.DEGs.add.rB.rR500.v3.0anno
# A tibble: 23 x 11
      X1 genes  logFC  logCPM    LR  PValue     FDR AGI   At_symbol
   <int> <chr>  <dbl>   <dbl> <dbl>   <dbl>   <dbl> <chr> <chr>    
 1     1 BraA…  1.42   2.28    32.0 1.53e-8 4.27e-4 AT5G… <NA>     
 2     2 BraA…  1.99   1.62    26.6 2.46e-7 3.43e-3 AT4G… CYP82C4  
 3     3 BraA…  0.941  2.67    24.2 8.86e-7 7.05e-3 AT3G… <NA>     
 4     4 BraA…  1.81   1.53    23.9 1.01e-6 7.05e-3 AT4G… ATIRT1   
 5     5 BraA…  1.67   0.0566  20.8 5.15e-6 2.73e-2 AT1G… <NA>     
 6     6 BraA…  1.43   0.469   20.5 5.87e-6 2.73e-2 AT2G… Iqd4     
 7     7 BraA…  1.42   2.16    19.9 8.24e-6 3.28e-2 AT2G… <NA>     
 8     8 BraA…  1.45   3.39    19.5 1.02e-5 3.28e-2 AT5G… <NA>     
 9     9 BraA…  1.47   2.36    19.2 1.16e-5 3.28e-2 AT5G… ATPT4    
10    10 BraA… -4.78  -0.507   19.1 1.26e-5 3.28e-2 <NA>  <NA>     
# ... with 13 more rows, and 2 more variables: At_short_description <chr>,
#   perc_ID <dbl>

$root.trt5E_dead.genotypeFPsc_trt5E_dead.DEGs.int.rB.rR500.v3.0anno
# A tibble: 40 x 12
      X1 genes logFC.trt5E_dead logFC.genotypeF… logCPM    LR  PValue
   <int> <chr>            <dbl>            <dbl>  <dbl> <dbl>   <dbl>
 1     1 BraA…          -0.0755           2.15    6.68   39.4 2.73e-9
 2     2 BraA…           0.797            1.55    1.62   37.3 8.04e-9
 3     3 BraA…           1.41             0.0163  2.28   30.9 1.99e-7
 4     4 BraA…           0.882            1.65    1.59   28.4 6.96e-7
 5     5 BraA…           0.770            1.39    3.39   27.0 1.38e-6
 6     6 BraA…          -0.174            1.33    2.87   26.4 1.82e-6
 7     7 BraA…          -0.0525          -3.86    2.45   26.3 1.93e-6
 8     8 BraA…           0.143            2.27    2.81   24.9 3.94e-6
 9     9 BraA…           0.901            1.15    0.469  24.2 5.61e-6
10    10 BraA…           0.0770           1.36    9.03   23.6 7.66e-6
# ... with 30 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$root.trt5E_dead.genotypeR500_trt5E_dead.DEGs.int.rB.rFPsc.v3.0anno
# A tibble: 40 x 12
      X1 genes logFC.trt5E_dead logFC.genotypeR… logCPM    LR  PValue
   <int> <chr>            <dbl>            <dbl>  <dbl> <dbl>   <dbl>
 1     1 BraA…             2.07          -2.15    6.68   39.4 2.73e-9
 2     2 BraA…             2.35          -1.55    1.62   37.3 8.04e-9
 3     3 BraA…             1.42          -0.0163  2.28   30.9 1.99e-7
 4     4 BraA…             2.53          -1.65    1.59   28.4 6.96e-7
 5     5 BraA…             2.16          -1.39    3.39   27.0 1.38e-6
 6     6 BraA…             1.16          -1.33    2.87   26.4 1.82e-6
 7     7 BraA…            -3.92           3.86    2.45   26.3 1.93e-6
 8     8 BraA…             2.41          -2.27    2.81   24.9 3.94e-6
 9     9 BraA…             2.06          -1.15    0.469  24.2 5.61e-6
10    10 BraA…             1.44          -1.36    9.03   23.6 7.66e-6
# ... with 30 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$root.trt5E_live.DEGs.add.rB.rFPsc.v3.0anno
# A tibble: 931 x 11
      X1 genes  logFC logCPM    LR   PValue     FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>    <dbl>   <dbl> <chr> <chr>    
 1     1 BraA… -1.28   2.79   48.3 3.58e-12 9.97e-8 AT2G… <NA>     
 2     2 BraA… -0.853  7.44   39.7 2.94e-10 4.10e-6 AT3G… AtDJ1A   
 3     3 BraA… -1.01   5.65   38.3 6.09e-10 5.66e-6 AT1G… AtNIGT1  
 4     4 BraA… -0.728  6.87   36.3 1.71e- 9 1.19e-5 AT3G… AtDJ1A   
 5     5 BraA…  1.11   3.16   33.4 7.41e- 9 4.13e-5 AT4G… AAT1     
 6     6 BraA…  2.09   1.69   32.9 9.58e- 9 4.45e-5 AT1G… PHT1;8   
 7     7 BraA…  1.41   0.714  30.2 3.96e- 8 1.58e-4 AT1G… <NA>     
 8     8 BraA…  1.30   2.16   29.4 5.96e- 8 2.08e-4 AT5G… AtMYB19  
 9     9 BraA…  1.12   1.66   28.4 9.71e- 8 2.49e-4 AT4G… <NA>     
10    10 BraA…  1.23   3.30   28.3 1.02e- 7 2.49e-4 AT3G… LAC7     
# ... with 921 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.trt5E_live.DEGs.add.rB.rR500.v3.0anno
# A tibble: 931 x 11
      X1 genes  logFC logCPM    LR   PValue     FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>    <dbl>   <dbl> <chr> <chr>    
 1     1 BraA… -1.28   2.79   48.3 3.58e-12 9.97e-8 AT2G… <NA>     
 2     2 BraA… -0.853  7.44   39.7 2.94e-10 4.10e-6 AT3G… AtDJ1A   
 3     3 BraA… -1.01   5.65   38.3 6.09e-10 5.66e-6 AT1G… AtNIGT1  
 4     4 BraA… -0.728  6.87   36.3 1.71e- 9 1.19e-5 AT3G… AtDJ1A   
 5     5 BraA…  1.11   3.16   33.4 7.41e- 9 4.13e-5 AT4G… AAT1     
 6     6 BraA…  2.09   1.69   32.9 9.58e- 9 4.45e-5 AT1G… PHT1;8   
 7     7 BraA…  1.41   0.714  30.2 3.96e- 8 1.58e-4 AT1G… <NA>     
 8     8 BraA…  1.30   2.16   29.4 5.96e- 8 2.08e-4 AT5G… AtMYB19  
 9     9 BraA…  1.12   1.66   28.4 9.71e- 8 2.49e-4 AT4G… <NA>     
10    10 BraA…  1.23   3.30   28.3 1.02e- 7 2.49e-4 AT3G… LAC7     
# ... with 921 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.trt5E_live.DEGs.add.rD.rFPsc.v3.0anno
# A tibble: 26 x 11
      X1 genes  logFC logCPM    LR  PValue     FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>   <dbl>   <dbl> <chr> <chr>    
 1     1 BraA… -1.37    2.49  35.6 2.39e-9 6.66e-5 AT3G… BHLH039  
 2     2 BraA… -1.38    1.82  31.6 1.93e-8 2.20e-4 AT3G… BHLH039  
 3     3 BraA… -0.754   7.44  31.2 2.37e-8 2.20e-4 AT3G… AtDJ1A   
 4     4 BraA… -0.648   6.87  28.8 7.97e-8 5.56e-4 AT3G… AtDJ1A   
 5     5 BraA… -0.600   5.31  27.9 1.30e-7 7.24e-4 AT4G… UGT73B1  
 6     6 BraA… -0.616   5.60  27.0 2.02e-7 9.37e-4 AT4G… UGT73B1  
 7     7 BraA…  1.21    2.58  26.2 3.10e-7 1.04e-3 AT1G… TAR4     
 8     8 BraA… -0.831   5.65  26.1 3.26e-7 1.04e-3 AT1G… AtNIGT1  
 9     9 BraA…  1.69    3.06  26.0 3.37e-7 1.04e-3 AT1G… <NA>     
10    10 BraA… -1.10    7.15  24.8 6.25e-7 1.74e-3 AT1G… <NA>     
# ... with 16 more rows, and 2 more variables: At_short_description <chr>,
#   perc_ID <dbl>

$root.trt5E_live.DEGs.add.rD.rR500.v3.0anno
# A tibble: 26 x 11
      X1 genes  logFC logCPM    LR  PValue     FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>   <dbl>   <dbl> <chr> <chr>    
 1     1 BraA… -1.37    2.49  35.6 2.39e-9 6.66e-5 AT3G… BHLH039  
 2     2 BraA… -1.38    1.82  31.6 1.93e-8 2.20e-4 AT3G… BHLH039  
 3     3 BraA… -0.754   7.44  31.2 2.37e-8 2.20e-4 AT3G… AtDJ1A   
 4     4 BraA… -0.648   6.87  28.8 7.97e-8 5.56e-4 AT3G… AtDJ1A   
 5     5 BraA… -0.600   5.31  27.9 1.30e-7 7.24e-4 AT4G… UGT73B1  
 6     6 BraA… -0.616   5.60  27.0 2.02e-7 9.37e-4 AT4G… UGT73B1  
 7     7 BraA…  1.21    2.58  26.2 3.10e-7 1.04e-3 AT1G… TAR4     
 8     8 BraA… -0.831   5.65  26.1 3.26e-7 1.04e-3 AT1G… AtNIGT1  
 9     9 BraA…  1.69    3.06  26.0 3.37e-7 1.04e-3 AT1G… <NA>     
10    10 BraA… -1.10    7.15  24.8 6.25e-7 1.74e-3 AT1G… <NA>     
# ... with 16 more rows, and 2 more variables: At_short_description <chr>,
#   perc_ID <dbl>

$root.trt5E_live.genotypeFPsc_trt5E_live.DEGs.int.rB.rR500.v3.0anno
# A tibble: 608 x 12
      X1 genes logFC.trt5E_live logFC.genotypeF… logCPM    LR   PValue
   <int> <chr>            <dbl>            <dbl>  <dbl> <dbl>    <dbl>
 1     1 BraA…           -1.45             0.859   5.65  53.8 2.04e-12
 2     2 BraA…           -1.55             0.526   2.79  53.2 2.87e-12
 3     3 BraA…           -0.697           -1.05    7.15  44.3 2.45e-10
 4     4 BraA…           -0.663           -0.389   7.44  42.9 4.75e-10
 5     5 BraA…           -0.556           -0.349   6.87  38.8 3.76e- 9
 6     6 BraA…            1.06             1.83    1.59  38.6 4.18e- 9
 7     7 BraA…            1.73            -0.931   2.16  38.6 4.25e- 9
 8     8 BraA…            0.900            0.654   3.16  37.9 5.79e- 9
 9     9 BraA…            0.946            1.34    5.01  36.4 1.23e- 8
10    10 BraA…            0.527            0.753   4.69  35.9 1.61e- 8
# ... with 598 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$root.trt5E_live.genotypeFPsc_trt5E_live.DEGs.int.rD.rR500.v3.0anno
# A tibble: 77 x 12
      X1 genes logFC.trt5E_live logFC.genotypeF… logCPM    LR   PValue
   <int> <chr>            <dbl>            <dbl>  <dbl> <dbl>    <dbl>
 1     1 BraA…           -0.538           -1.21   7.15   41.7 8.66e-10
 2     2 BraA…           -1.14             0.590  5.65   35.9 1.59e- 8
 3     3 BraA…           -1.50             0.191  2.49   35.1 2.43e- 8
 4     4 BraA…           -0.581           -0.358  7.44   33.9 4.30e- 8
 5     5 BraA…            2.22            -2.33   1.23   33.7 4.91e- 8
 6     6 BraA…            1.57            -1.36   4.01   31.8 1.26e- 7
 7     7 BraA…           -0.836           -1.91   0.848  31.7 1.32e- 7
 8     8 BraA…           -1.58             0.333  1.82   31.2 1.66e- 7
 9     9 BraA…           -0.529           -0.246  6.87   30.4 2.55e- 7
10    10 BraA…            1.69            -1.46   3.49   29.9 3.29e- 7
# ... with 67 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$root.trt5E_live.genotypeFPsc.DEGs.int.rB.rR500.v3.0anno
# A tibble: 4 x 11
     X1 genes logFC logCPM    LR  PValue     FDR AGI   At_symbol
  <int> <chr> <dbl>  <dbl> <dbl>   <dbl>   <dbl> <chr> <chr>    
1     1 BraA… -4.86  4.91   25.7 3.90e-7 0.00548 AT1G… ATU2AF65B
2     2 BraA…  3.42  0.428  25.7 3.93e-7 0.00548 AT5G… <NA>     
3     3 BraA… -1.55  1.93   20.4 6.29e-6 0.0453  AT4G… UBC17    
4     4 BraA…  2.02  6.68   20.3 6.50e-6 0.0453  AT4G… <NA>     
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>

$root.trt5E_live.genotypeFPsc.DEGs.int.rD.rR500.v3.0anno
# A tibble: 2 x 11
     X1 genes logFC logCPM    LR  PValue    FDR AGI   At_symbol
  <int> <chr> <dbl>  <dbl> <dbl>   <dbl>  <dbl> <chr> <chr>    
1     1 BraA…  3.28  1.39   23.8 1.05e-6 0.0293 AT3G… <NA>     
2     2 BraA…  2.95  0.428  21.5 3.55e-6 0.0495 AT5G… <NA>     
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>

$root.trt5E_live.genotypeR500_trt5E_live.DEGs.int.rB.rFPsc.v3.0anno
# A tibble: 608 x 12
      X1 genes logFC.trt5E_live logFC.genotypeR… logCPM    LR   PValue
   <int> <chr>            <dbl>            <dbl>  <dbl> <dbl>    <dbl>
 1     1 BraA…           -0.590           -0.859   5.65  53.8 2.04e-12
 2     2 BraA…           -1.03            -0.526   2.79  53.2 2.87e-12
 3     3 BraA…           -1.74             1.05    7.15  44.3 2.45e-10
 4     4 BraA…           -1.05             0.389   7.44  42.9 4.75e-10
 5     5 BraA…           -0.905            0.349   6.87  38.8 3.76e- 9
 6     6 BraA…            2.89            -1.83    1.59  38.6 4.18e- 9
 7     7 BraA…            0.799            0.931   2.16  38.6 4.25e- 9
 8     8 BraA…            1.55            -0.654   3.16  37.9 5.79e- 9
 9     9 BraA…            2.29            -1.34    5.01  36.4 1.23e- 8
10    10 BraA…            1.28            -0.753   4.69  35.9 1.61e- 8
# ... with 598 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$root.trt5E_live.genotypeR500_trt5E_live.DEGs.int.rD.rFPsc.v3.0anno
# A tibble: 77 x 12
      X1 genes logFC.trt5E_live logFC.genotypeR… logCPM    LR   PValue
   <int> <chr>            <dbl>            <dbl>  <dbl> <dbl>    <dbl>
 1     1 BraA…           -1.75             1.21   7.15   41.7 8.66e-10
 2     2 BraA…           -0.554           -0.590  5.65   35.9 1.59e- 8
 3     3 BraA…           -1.31            -0.191  2.49   35.1 2.43e- 8
 4     4 BraA…           -0.939            0.358  7.44   33.9 4.30e- 8
 5     5 BraA…           -0.113            2.33   1.23   33.7 4.91e- 8
 6     6 BraA…            0.211            1.36   4.01   31.8 1.26e- 7
 7     7 BraA…           -2.75             1.91   0.848  31.7 1.32e- 7
 8     8 BraA…           -1.25            -0.333  1.82   31.2 1.66e- 7
 9     9 BraA…           -0.775            0.246  6.87   30.4 2.55e- 7
10    10 BraA…            0.236            1.46   3.49   29.9 3.29e- 7
# ... with 67 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$root.trt5E_live.genotypeR500.DEGs.int.rB.rFPsc.v3.0anno
# A tibble: 4 x 11
     X1 genes logFC logCPM    LR  PValue     FDR AGI   At_symbol
  <int> <chr> <dbl>  <dbl> <dbl>   <dbl>   <dbl> <chr> <chr>    
1     1 BraA…  4.86  4.91   25.7 3.90e-7 0.00548 AT1G… ATU2AF65B
2     2 BraA… -3.42  0.428  25.7 3.93e-7 0.00548 AT5G… <NA>     
3     3 BraA…  1.55  1.93   20.4 6.29e-6 0.0453  AT4G… UBC17    
4     4 BraA… -2.02  6.68   20.3 6.50e-6 0.0453  AT4G… <NA>     
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>
lapply(DEG.count.list.e1.v3.0annotation.all,function(df) filter(df,FDR<0.05)) # does work
$leaf.FPsc.trtlive.DEGs.all.rD.v3.0anno
# A tibble: 2 x 11
     X1 genes logFC logCPM    LR  PValue     FDR AGI   At_symbol
  <int> <chr> <dbl>  <dbl> <dbl>   <dbl>   <dbl> <chr> <chr>    
1     1 BraA…  2.06  0.119  28.2 1.10e-7 0.00256 AT3G… <NA>     
2     2 BraA…  2.44  0.460  24.1 9.03e-7 0.0105  AT1G… AtVTL1   
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>

$leaf.genotypeFPsc_trt5E_live.genotypeFPsc_trt5E_dead.genotypeFPsc.DEGs.int.rB.rR500.v3.0anno
# A tibble: 18,895 x 13
      X1 genes logFC.genotypeF… logFC.genotypeF… logFC.genotypeF… logCPM
   <int> <chr>            <dbl>            <dbl>            <dbl>  <dbl>
 1     1 BraA…            -13.1           1.28             1.76     6.28
 2     2 BraA…            -12.4           0.829            0.0153   6.99
 3     3 BraA…             12.1          -0.791            1.16     6.40
 4     4 BraA…            -12.1          -0.0737           0.114    5.28
 5     5 BraA…            -12.1          -0.201           -0.825    6.50
 6     6 BraA…            -12.0           1.20            -0.163    5.28
 7     7 BraA…            -11.8           2.08             2.81     4.84
 8     8 BraA…             11.7          -1.18            -0.702    6.97
 9     9 BraA…            -11.7          -0.149           -0.115    4.94
10    10 BraA…            -11.6           0.0524           0.0330   4.78
# ... with 18,885 more rows, and 7 more variables: LR <dbl>, PValue <dbl>,
#   FDR <dbl>, AGI <chr>, At_symbol <chr>, At_short_description <chr>,
#   perc_ID <dbl>

$leaf.genotypeFPsc_trt5E_live.genotypeFPsc_trtBLANK_NA.genotypeFPsc.DEGs.int.rD.rR500.v3.0anno
# A tibble: 18,895 x 13
      X1 genes logFC.genotypeF… logFC.genotypeF… logFC.genotypeF… logCPM
   <int> <chr>            <dbl>            <dbl>            <dbl>  <dbl>
 1     1 BraA…            -13.3           2.23             3.29     6.34
 2     2 BraA…             12.8          -1.76            -1.60     5.99
 3     3 BraA…            -12.3           0.201           -0.624    6.50
 4     4 BraA…            -12.2           0.0737           0.188    5.28
 5     5 BraA…             12.1          -1.17            -1.38     5.13
 6     6 BraA…            -11.9           1.27             1.98     5.04
 7     7 BraA…            -11.8           0.149            0.0341   4.94
 8     8 BraA…            -11.8          -1.28             0.481    6.28
 9     9 BraA…            -11.6          -0.0524          -0.0194   4.78
10    10 BraA…            -11.5          -0.829           -0.814    6.99
# ... with 18,885 more rows, and 7 more variables: LR <dbl>, PValue <dbl>,
#   FDR <dbl>, AGI <chr>, At_symbol <chr>, At_short_description <chr>,
#   perc_ID <dbl>

$leaf.genotypeFPsc.DEGs.add.rB.rR500.v3.0anno
# A tibble: 19,658 x 11
      X1 genes logFC logCPM    LR PValue   FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>  <dbl> <dbl> <chr> <chr>    
 1     1 BraA… -12.4   6.50 2505.      0     0 AT1G… TAR4     
 2     2 BraA… -12.1   5.28 4344.      0     0 <NA>  <NA>     
 3     3 BraA…  12.1   6.40 3411.      0     0 AT2G… ATCNGC11 
 4     4 BraA… -12.1   6.99 1955.      0     0 AT4G… CRK39    
 5     5 BraA… -11.9   6.28 1578.      0     0 AT1G… ATBBD1   
 6     6 BraA… -11.8   4.94 1986.      0     0 <NA>  <NA>     
 7     7 BraA… -11.6   4.78 3000.      0     0 <NA>  <NA>     
 8     8 BraA… -11.6   5.28 3458.      0     0 AT1G… <NA>     
 9     9 BraA… -11.5   4.63 2430.      0     0 AT5G… <NA>     
10    10 BraA…  11.4   5.99 5024.      0     0 <NA>  <NA>     
# ... with 19,648 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$leaf.genotypeFPsc.DEGs.add.rD.rR500.v3.0anno
# A tibble: 19,658 x 11
      X1 genes logFC logCPM    LR PValue   FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>  <dbl> <dbl> <chr> <chr>    
 1     1 BraA… -12.4   6.50 2505.      0     0 AT1G… TAR4     
 2     2 BraA… -12.1   5.28 4344.      0     0 <NA>  <NA>     
 3     3 BraA…  12.1   6.40 3411.      0     0 AT2G… ATCNGC11 
 4     4 BraA… -12.1   6.99 1955.      0     0 AT4G… CRK39    
 5     5 BraA… -11.9   6.28 1578.      0     0 AT1G… ATBBD1   
 6     6 BraA… -11.8   4.94 1986.      0     0 <NA>  <NA>     
 7     7 BraA… -11.6   4.78 3000.      0     0 <NA>  <NA>     
 8     8 BraA… -11.6   5.28 3458.      0     0 AT1G… <NA>     
 9     9 BraA… -11.5   4.63 2430.      0     0 AT5G… <NA>     
10    10 BraA…  11.4   5.99 5024.      0     0 <NA>  <NA>     
# ... with 19,648 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$leaf.genotypeR500_trt5E_live.genotypeR500_trt5E_dead.genotypeR500.DEGs.int.rB.rFPsc.v3.0anno
# A tibble: 18,895 x 13
      X1 genes logFC.genotypeR… logFC.genotypeR… logFC.genotypeR… logCPM
   <int> <chr>            <dbl>            <dbl>            <dbl>  <dbl>
 1     1 BraA…             13.1          -1.28            -1.76     6.28
 2     2 BraA…             12.4          -0.829           -0.0153   6.99
 3     3 BraA…            -12.1           0.791           -1.16     6.40
 4     4 BraA…             12.1           0.0737          -0.114    5.28
 5     5 BraA…             12.1           0.201            0.825    6.50
 6     6 BraA…             12.0          -1.20             0.163    5.28
 7     7 BraA…             11.8          -2.08            -2.81     4.84
 8     8 BraA…            -11.7           1.18             0.702    6.97
 9     9 BraA…             11.7           0.149            0.115    4.94
10    10 BraA…             11.6          -0.0524          -0.0330   4.78
# ... with 18,885 more rows, and 7 more variables: LR <dbl>, PValue <dbl>,
#   FDR <dbl>, AGI <chr>, At_symbol <chr>, At_short_description <chr>,
#   perc_ID <dbl>

$leaf.genotypeR500_trt5E_live.genotypeR500_trtBLANK_NA.genotypeR500.DEGs.int.rD.rFPsc.v3.0anno
# A tibble: 18,895 x 13
      X1 genes logFC.genotypeR… logFC.genotypeR… logFC.genotypeR… logCPM
   <int> <chr>            <dbl>            <dbl>            <dbl>  <dbl>
 1     1 BraA…             13.3          -2.23            -3.29     6.34
 2     2 BraA…            -12.8           1.76             1.60     5.99
 3     3 BraA…             12.3          -0.201            0.624    6.50
 4     4 BraA…             12.2          -0.0737          -0.188    5.28
 5     5 BraA…            -12.1           1.17             1.38     5.13
 6     6 BraA…             11.9          -1.27            -1.98     5.04
 7     7 BraA…             11.8          -0.149           -0.0341   4.94
 8     8 BraA…             11.8           1.28            -0.481    6.28
 9     9 BraA…             11.6           0.0524           0.0194   4.78
10    10 BraA…             11.5           0.829            0.814    6.99
# ... with 18,885 more rows, and 7 more variables: LR <dbl>, PValue <dbl>,
#   FDR <dbl>, AGI <chr>, At_symbol <chr>, At_short_description <chr>,
#   perc_ID <dbl>

$leaf.genotypeR500.DEGs.add.rB.rFPsc.v3.0anno
# A tibble: 19,658 x 11
      X1 genes logFC logCPM    LR PValue   FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>  <dbl> <dbl> <chr> <chr>    
 1     1 BraA…  12.4   6.50 2505.      0     0 AT1G… TAR4     
 2     2 BraA…  12.1   5.28 4344.      0     0 <NA>  <NA>     
 3     3 BraA… -12.1   6.40 3411.      0     0 AT2G… ATCNGC11 
 4     4 BraA…  12.1   6.99 1955.      0     0 AT4G… CRK39    
 5     5 BraA…  11.9   6.28 1578.      0     0 AT1G… ATBBD1   
 6     6 BraA…  11.8   4.94 1986.      0     0 <NA>  <NA>     
 7     7 BraA…  11.6   4.78 3000.      0     0 <NA>  <NA>     
 8     8 BraA…  11.6   5.28 3458.      0     0 AT1G… <NA>     
 9     9 BraA…  11.5   4.63 2430.      0     0 AT5G… <NA>     
10    10 BraA… -11.4   5.99 5024.      0     0 <NA>  <NA>     
# ... with 19,648 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$leaf.genotypeR500.DEGs.add.rD.rFPsc.v3.0anno
# A tibble: 19,658 x 11
      X1 genes logFC logCPM    LR PValue   FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>  <dbl> <dbl> <chr> <chr>    
 1     1 BraA…  12.4   6.50 2505.      0     0 AT1G… TAR4     
 2     2 BraA…  12.1   5.28 4344.      0     0 <NA>  <NA>     
 3     3 BraA… -12.1   6.40 3411.      0     0 AT2G… ATCNGC11 
 4     4 BraA…  12.1   6.99 1955.      0     0 AT4G… CRK39    
 5     5 BraA…  11.9   6.28 1578.      0     0 AT1G… ATBBD1   
 6     6 BraA…  11.8   4.94 1986.      0     0 <NA>  <NA>     
 7     7 BraA…  11.6   4.78 3000.      0     0 <NA>  <NA>     
 8     8 BraA…  11.6   5.28 3458.      0     0 AT1G… <NA>     
 9     9 BraA…  11.5   4.63 2430.      0     0 AT5G… <NA>     
10    10 BraA… -11.4   5.99 5024.      0     0 <NA>  <NA>     
# ... with 19,648 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$leaf.R500.trtlive.DEGs.all.rD.v3.0anno
# A tibble: 1,927 x 11
      X1 genes logFC logCPM    LR   PValue      FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>    <dbl>    <dbl> <chr> <chr>    
 1     1 BraA… -2.06   5.13  64.4 9.98e-16 2.40e-11 AT2G… ATP5CS   
 2     2 BraA… -1.55   5.25  42.0 9.02e-11 1.09e- 6 AT5G… AtcPT4   
 3     3 BraA… -1.67   2.22  37.2 1.04e- 9 8.35e- 6 AT1G… ATGSTU25 
 4     4 BraA… -1.18   3.93  36.1 1.86e- 9 1.12e- 5 AT2G… ANNAT4   
 5     5 BraA… -2.08   1.98  35.7 2.33e- 9 1.12e- 5 AT5G… <NA>     
 6     6 BraA…  2.53   3.65  34.3 4.63e- 9 1.86e- 5 AT3G… CYP72A8  
 7     7 BraA… -1.63   1.89  33.7 6.36e- 9 2.19e- 5 AT5G… <NA>     
 8     8 BraA… -1.94   7.40  32.9 9.50e- 9 2.86e- 5 AT3G… UGP3     
 9     9 BraA… -2.93   2.43  32.6 1.10e- 8 2.95e- 5 AT1G… AtPFA-DS…
10    10 BraA… -2.27   6.82  32.4 1.24e- 8 2.99e- 5 AT1G… ATPPCK1  
# ... with 1,917 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$leaf.trt5E_dead.DEGs.add.rB.rFPsc.v3.0anno
# A tibble: 0 x 11
# ... with 11 variables: X1 <int>, genes <chr>, logFC <dbl>, logCPM <dbl>,
#   LR <dbl>, PValue <dbl>, FDR <dbl>, AGI <chr>, At_symbol <chr>,
#   At_short_description <chr>, perc_ID <dbl>

$leaf.trt5E_dead.DEGs.add.rB.rR500.v3.0anno
# A tibble: 0 x 11
# ... with 11 variables: X1 <int>, genes <chr>, logFC <dbl>, logCPM <dbl>,
#   LR <dbl>, PValue <dbl>, FDR <dbl>, AGI <chr>, At_symbol <chr>,
#   At_short_description <chr>, perc_ID <dbl>

$leaf.trt5E_dead.genotypeFPsc_trt5E_dead.DEGs.int.rB.rR500.v3.0anno
# A tibble: 2 x 12
     X1 genes logFC.trt5E_dead logFC.genotypeF… logCPM    LR  PValue
  <int> <chr>            <dbl>            <dbl>  <dbl> <dbl>   <dbl>
1     1 BraA…             1.31            -1.19   4.33  30.4 2.49e-7
2     2 BraA…             5.60            -5.46   3.93  30.4 2.56e-7
# ... with 5 more variables: FDR <dbl>, AGI <chr>, At_symbol <chr>,
#   At_short_description <chr>, perc_ID <dbl>

$leaf.trt5E_dead.genotypeR500_trt5E_dead.DEGs.int.rB.rFPsc.v3.0anno
# A tibble: 2 x 12
     X1 genes logFC.trt5E_dead logFC.genotypeR… logCPM    LR  PValue
  <int> <chr>            <dbl>            <dbl>  <dbl> <dbl>   <dbl>
1     1 BraA…            0.124             1.19   4.33  30.4 2.49e-7
2     2 BraA…            0.142             5.46   3.93  30.4 2.56e-7
# ... with 5 more variables: FDR <dbl>, AGI <chr>, At_symbol <chr>,
#   At_short_description <chr>, perc_ID <dbl>

$leaf.trt5E_live.DEGs.add.rB.rFPsc.v3.0anno
# A tibble: 144 x 11
      X1 genes  logFC logCPM    LR  PValue     FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>   <dbl>   <dbl> <chr> <chr>    
 1     1 BraA…  0.617  3.31   29.9 4.54e-8 0.00114 AT1G… <NA>     
 2     2 BraA… -1.74   3.55   28.1 1.16e-7 0.00146 AT1G… AtWSCP   
 3     3 BraA…  0.579  3.07   24.4 7.75e-7 0.00619 AT5G… ATHIR1   
 4     4 BraA… -1.30   0.169  24.0 9.82e-7 0.00619 AT1G… GXM1     
 5     5 BraA… -0.573  5.72   22.0 2.77e-6 0.00936 AT1G… ADT1     
 6     6 BraA… -0.625  3.09   21.9 2.82e-6 0.00936 AT4G… GrxC5    
 7     7 BraA… -0.615  3.75   21.7 3.13e-6 0.00936 AT2G… ALF1     
 8     8 BraA… -1.63   2.99   21.7 3.26e-6 0.00936 AT1G… <NA>     
 9     9 BraA…  1.52  -0.158  21.6 3.34e-6 0.00936 AT4G… ATK5     
10    10 BraA… -0.550  3.01   20.9 4.91e-6 0.0124  AT5G… <NA>     
# ... with 134 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$leaf.trt5E_live.DEGs.add.rB.rR500.v3.0anno
# A tibble: 144 x 11
      X1 genes  logFC logCPM    LR  PValue     FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>   <dbl>   <dbl> <chr> <chr>    
 1     1 BraA…  0.617  3.31   29.9 4.54e-8 0.00114 AT1G… <NA>     
 2     2 BraA… -1.74   3.55   28.1 1.16e-7 0.00146 AT1G… AtWSCP   
 3     3 BraA…  0.579  3.07   24.4 7.75e-7 0.00619 AT5G… ATHIR1   
 4     4 BraA… -1.30   0.169  24.0 9.82e-7 0.00619 AT1G… GXM1     
 5     5 BraA… -0.573  5.72   22.0 2.77e-6 0.00936 AT1G… ADT1     
 6     6 BraA… -0.625  3.09   21.9 2.82e-6 0.00936 AT4G… GrxC5    
 7     7 BraA… -0.615  3.75   21.7 3.13e-6 0.00936 AT2G… ALF1     
 8     8 BraA… -1.63   2.99   21.7 3.26e-6 0.00936 AT1G… <NA>     
 9     9 BraA…  1.52  -0.158  21.6 3.34e-6 0.00936 AT4G… ATK5     
10    10 BraA… -0.550  3.01   20.9 4.91e-6 0.0124  AT5G… <NA>     
# ... with 134 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$leaf.trt5E_live.DEGs.add.rD.rFPsc.v3.0anno
# A tibble: 1,932 x 11
      X1 genes  logFC logCPM    LR   PValue     FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>    <dbl>   <dbl> <chr> <chr>    
 1     1 BraA… -1.63   1.26   38.1 6.58e-10 1.66e-5 AT1G… ATGSTU25 
 2     2 BraA… -1.88   3.55   32.3 1.29e- 8 1.44e-4 AT1G… AtWSCP   
 3     3 BraA… -0.737  3.75   31.1 2.45e- 8 1.44e-4 AT2G… ALF1     
 4     4 BraA…  1.25   0.725  31.0 2.56e- 8 1.44e-4 <NA>  <NA>     
 5     5 BraA…  0.889  5.15   30.8 2.85e- 8 1.44e-4 AT5G… <NA>     
 6     6 BraA…  0.841  3.81   30.2 3.85e- 8 1.62e-4 AT5G… <NA>     
 7     7 BraA…  1.44   1.69   29.8 4.91e- 8 1.77e-4 AT1G… SMR2     
 8     8 BraA…  1.80   1.28   27.9 1.26e- 7 3.96e-4 AT3G… <NA>     
 9     9 BraA…  0.537  3.28   27.6 1.51e- 7 4.22e-4 AT5G… ATFIP1[V]
10    10 BraA… -0.370  5.90   26.9 2.18e- 7 5.36e-4 AT1G… ARC12    
# ... with 1,922 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$leaf.trt5E_live.DEGs.add.rD.rR500.v3.0anno
# A tibble: 1,932 x 11
      X1 genes  logFC logCPM    LR   PValue     FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>    <dbl>   <dbl> <chr> <chr>    
 1     1 BraA… -1.63   1.26   38.1 6.58e-10 1.66e-5 AT1G… ATGSTU25 
 2     2 BraA… -1.88   3.55   32.3 1.29e- 8 1.44e-4 AT1G… AtWSCP   
 3     3 BraA… -0.737  3.75   31.1 2.45e- 8 1.44e-4 AT2G… ALF1     
 4     4 BraA…  1.25   0.725  31.0 2.56e- 8 1.44e-4 <NA>  <NA>     
 5     5 BraA…  0.889  5.15   30.8 2.85e- 8 1.44e-4 AT5G… <NA>     
 6     6 BraA…  0.841  3.81   30.2 3.85e- 8 1.62e-4 AT5G… <NA>     
 7     7 BraA…  1.44   1.69   29.8 4.91e- 8 1.77e-4 AT1G… SMR2     
 8     8 BraA…  1.80   1.28   27.9 1.26e- 7 3.96e-4 AT3G… <NA>     
 9     9 BraA…  0.537  3.28   27.6 1.51e- 7 4.22e-4 AT5G… ATFIP1[V]
10    10 BraA… -0.370  5.90   26.9 2.18e- 7 5.36e-4 AT1G… ARC12    
# ... with 1,922 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$leaf.trt5E_live.genotypeFPsc_trt5E_live.DEGs.int.rB.rR500.v3.0anno
# A tibble: 399 x 12
      X1 genes logFC.trt5E_live logFC.genotypeF… logCPM    LR   PValue
   <int> <chr>            <dbl>            <dbl>  <dbl> <dbl>    <dbl>
 1     1 BraA…           -1.44             1.44    3.15  45.2 1.53e-10
 2     2 BraA…           -0.107            4.00    1.98  37.2 8.22e- 9
 3     3 BraA…            0.503            0.261   3.31  31.4 1.53e- 7
 4     4 BraA…           -5.55             4.85    6.89  30.8 2.02e- 7
 5     5 BraA…           -2.03             2.06    3.23  30.4 2.55e- 7
 6     6 BraA…           -0.842            0.719   7.36  29.9 3.24e- 7
 7     7 BraA…           -1.26             1.05    4.67  29.8 3.32e- 7
 8     8 BraA…           -1.73             1.82    2.32  29.7 3.54e- 7
 9     9 BraA…            5.51            -5.39    3.93  29.1 4.72e- 7
10    10 BraA…           -1.77             1.82    3.55  28.3 7.33e- 7
# ... with 389 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$leaf.trt5E_live.genotypeFPsc_trt5E_live.DEGs.int.rD.rR500.v3.0anno
# A tibble: 2,061 x 12
      X1 genes logFC.trt5E_live logFC.genotypeF… logCPM    LR   PValue
   <int> <chr>            <dbl>            <dbl>  <dbl> <dbl>    <dbl>
 1     1 BraA…            -2.05            2.10    4.33  69.8 6.82e-16
 2     2 BraA…            -2.93            2.85    2.99  50.6 1.05e-11
 3     3 BraA…             1.36           -1.10    4.25  45.3 1.44e-10
 4     4 BraA…            -2.25            1.85    7.95  44.9 1.77e-10
 5     5 BraA…            -1.06            0.665   3.75  44.7 1.94e-10
 6     6 BraA…            -2.43            1.96    3.99  42.5 5.87e-10
 7     7 BraA…             2.36           -2.08    3.32  40.7 1.48e- 9
 8     8 BraA…             1.22           -0.692   5.15  38.5 4.34e- 9
 9     9 BraA…            -1.67            1.09    1.26  38.2 4.98e- 9
10    10 BraA…            -4.17            3.88    3.53  37.6 6.82e- 9
# ... with 2,051 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$leaf.trt5E_live.genotypeFPsc.DEGs.int.rB.rR500.v3.0anno
# A tibble: 5 x 11
     X1 genes logFC logCPM    LR  PValue     FDR AGI   At_symbol
  <int> <chr> <dbl>  <dbl> <dbl>   <dbl>   <dbl> <chr> <chr>    
1     1 BraA…  4.00   1.98  34.5 4.19e-9 1.06e-4 <NA>  <NA>     
2     2 BraA… -5.39   3.93  21.6 3.33e-6 2.89e-2 AT1G… ATU2AF65B
3     3 BraA…  1.44   3.15  21.6 3.43e-6 2.89e-2 AT1G… ASB1     
4     4 BraA… -4.43   2.62  20.2 7.13e-6 4.50e-2 AT2G… ATPEX10  
5     5 BraA…  2.41   2.99  19.6 9.72e-6 4.90e-2 AT1G… AtPFA-DS…
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>

$leaf.trt5E_live.genotypeFPsc.DEGs.int.rD.rR500.v3.0anno
# A tibble: 8 x 11
     X1 genes logFC logCPM    LR   PValue     FDR AGI   At_symbol
  <int> <chr> <dbl>  <dbl> <dbl>    <dbl>   <dbl> <chr> <chr>    
1     1 BraA…  2.10   4.33  35.4  2.65e-9 6.68e-5 AT2G… ATP5CS   
2     2 BraA…  3.21   2.98  31.8  1.72e-8 2.17e-4 AT5G… ABCF2    
3     3 BraA…  2.85   2.99  27.7  1.43e-7 1.20e-3 AT1G… AtPFA-DS…
4     4 BraA…  1.72   5.63  22.7  1.91e-6 1.20e-2 AT5G… AtcPT4   
5     5 BraA… -3.46   2.58  21.0  4.51e-6 2.27e-2 AT1G… ATGPT2   
6     6 BraA…  3.88   3.53  19.8  8.40e-6 3.53e-2 AT3G… ATACP5   
7     7 BraA… -2.08   3.32  19.5 10.00e-6 3.60e-2 AT5G… <NA>     
8     8 BraA…  2.81   1.29  19.0  1.31e-5 4.14e-2 AT5G… <NA>     
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>

$leaf.trt5E_live.genotypeR500_trt5E_live.DEGs.int.rB.rFPsc.v3.0anno
# A tibble: 399 x 12
      X1 genes logFC.trt5E_live logFC.genotypeR… logCPM    LR   PValue
   <int> <chr>            <dbl>            <dbl>  <dbl> <dbl>    <dbl>
 1     1 BraA…          0.00152           -1.44    3.15  45.2 1.53e-10
 2     2 BraA…          3.89              -4.00    1.98  37.2 8.22e- 9
 3     3 BraA…          0.764             -0.261   3.31  31.4 1.53e- 7
 4     4 BraA…         -0.695             -4.85    6.89  30.8 2.02e- 7
 5     5 BraA…          0.0355            -2.06    3.23  30.4 2.55e- 7
 6     6 BraA…         -0.123             -0.719   7.36  29.9 3.24e- 7
 7     7 BraA…         -0.209             -1.05    4.67  29.8 3.32e- 7
 8     8 BraA…          0.0889            -1.82    2.32  29.7 3.54e- 7
 9     9 BraA…          0.117              5.39    3.93  29.1 4.72e- 7
10    10 BraA…          0.0435            -1.82    3.55  28.3 7.33e- 7
# ... with 389 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$leaf.trt5E_live.genotypeR500_trt5E_live.DEGs.int.rD.rFPsc.v3.0anno
# A tibble: 2,061 x 12
      X1 genes logFC.trt5E_live logFC.genotypeR… logCPM    LR   PValue
   <int> <chr>            <dbl>            <dbl>  <dbl> <dbl>    <dbl>
 1     1 BraA…           0.0565           -2.10    4.33  69.8 6.82e-16
 2     2 BraA…          -0.0794           -2.85    2.99  50.6 1.05e-11
 3     3 BraA…           0.263             1.10    4.25  45.3 1.44e-10
 4     4 BraA…          -0.407            -1.85    7.95  44.9 1.77e-10
 5     5 BraA…          -0.393            -0.665   3.75  44.7 1.94e-10
 6     6 BraA…          -0.471            -1.96    3.99  42.5 5.87e-10
 7     7 BraA…           0.286             2.08    3.32  40.7 1.48e- 9
 8     8 BraA…           0.523             0.692   5.15  38.5 4.34e- 9
 9     9 BraA…          -0.583            -1.09    1.26  38.2 4.98e- 9
10    10 BraA…          -0.288            -3.88    3.53  37.6 6.82e- 9
# ... with 2,051 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$leaf.trt5E_live.genotypeR500.DEGs.int.rB.rFPsc.v3.0anno
# A tibble: 5 x 11
     X1 genes logFC logCPM    LR  PValue     FDR AGI   At_symbol
  <int> <chr> <dbl>  <dbl> <dbl>   <dbl>   <dbl> <chr> <chr>    
1     1 BraA… -4.00   1.98  34.5 4.19e-9 1.06e-4 <NA>  <NA>     
2     2 BraA…  5.39   3.93  21.6 3.33e-6 2.89e-2 AT1G… ATU2AF65B
3     3 BraA… -1.44   3.15  21.6 3.43e-6 2.89e-2 AT1G… ASB1     
4     4 BraA…  4.43   2.62  20.2 7.13e-6 4.50e-2 AT2G… ATPEX10  
5     5 BraA… -2.41   2.99  19.6 9.72e-6 4.90e-2 AT1G… AtPFA-DS…
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>

$root.FPsc.trtlive.DEGs.all.rD.v3.0anno
# A tibble: 9 x 11
     X1 genes  logFC logCPM    LR   PValue     FDR AGI   At_symbol
  <int> <chr>  <dbl>  <dbl> <dbl>    <dbl>   <dbl> <chr> <chr>    
1     1 BraA… -1.70   5.74   37.9 7.54e-10 1.99e-5 AT1G… <NA>     
2     2 BraA… -2.70   0.746  27.1 1.92e- 7 2.53e-3 AT5G… CGLD27   
3     3 BraA…  4.90   4.78   24.9 6.18e- 7 5.43e-3 AT5G… HSP18.2  
4     4 BraA…  3.02   4.43   21.3 3.97e- 6 2.27e-2 AT5G… HSP18.2  
5     5 BraA… -1.05   7.43   21.1 4.30e- 6 2.27e-2 AT1G… ATOPR2   
6     6 BraA… -0.761  2.51   20.6 5.79e- 6 2.43e-2 AT1G… <NA>     
7     7 BraA…  2.53   0.780  20.3 6.46e- 6 2.43e-2 AT3G… <NA>     
8     8 BraA… -1.31   3.16   19.5 9.87e- 6 2.96e-2 AT3G… BHLH039  
9     9 BraA… -0.938  6.99   19.5 1.01e- 5 2.96e-2 AT3G… AtDJ1A   
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>

$root.genotypeFPsc_trt5E_live.genotypeFPsc_trt5E_dead.genotypeFPsc.DEGs.int.rB.rR500.v3.0anno
# A tibble: 17,373 x 13
      X1 genes logFC.genotypeF… logFC.genotypeF… logFC.genotypeF… logCPM
   <int> <chr>            <dbl>            <dbl>            <dbl>  <dbl>
 1     1 BraA…             14.4          -2.48            -2.08     7.57
 2     2 BraA…            -14.3           1.08             1.42     7.50
 3     3 BraA…             13.6          -1.30            -0.0224   6.77
 4     4 BraA…             13.0          -1.33            -1.99     6.18
 5     5 BraA…            -12.6           2.16             2.96     5.81
 6     6 BraA…             12.5          -4.21            -4.13     5.83
 7     7 BraA…             12.3          -0.131           -1.29     5.50
 8     8 BraA…             12.3          -1.42            -0.269    5.36
 9     9 BraA…             12.2           0.0831          -1.14     5.49
10    10 BraA…             12.1          -0.139           -2.13     5.21
# ... with 17,363 more rows, and 7 more variables: LR <dbl>, PValue <dbl>,
#   FDR <dbl>, AGI <chr>, At_symbol <chr>, At_short_description <chr>,
#   perc_ID <dbl>

$root.genotypeFPsc_trt5E_live.genotypeFPsc_trtBLANK_NA.genotypeFPsc.DEGs.int.rD.rR500.v3.0anno
# A tibble: 17,373 x 13
      X1 genes logFC.genotypeF… logFC.genotypeF… logFC.genotypeF… logCPM
   <int> <chr>            <dbl>            <dbl>            <dbl>  <dbl>
 1     1 BraA…             13.3          -1.28             0.0181   6.55
 2     2 BraA…            -13.2          -1.08             0.338    7.50
 3     3 BraA…            -13.2           1.76             1.23     6.43
 4     4 BraA…            -12.5           0.465            1.32     7.08
 5     5 BraA…             12.3          -0.0831          -1.22     5.49
 6     6 BraA…             12.2           1.30             1.28     6.77
 7     7 BraA…             12.2           0.131           -1.16     5.50
 8     8 BraA…            -12.0           1.24             1.70     5.33
 9     9 BraA…             12.0           0.139           -1.99     5.21
10    10 BraA…             11.9           2.48             0.395    7.57
# ... with 17,363 more rows, and 7 more variables: LR <dbl>, PValue <dbl>,
#   FDR <dbl>, AGI <chr>, At_symbol <chr>, At_short_description <chr>,
#   perc_ID <dbl>

$root.genotypeFPsc.DEGs.add.rB.rR500.v3.0anno
# A tibble: 18,989 x 11
      X1 genes logFC logCPM    LR PValue   FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>  <dbl> <dbl> <chr> <chr>    
 1     1 BraA… -13.4   7.50 3038.      0     0 AT1G… <NA>     
 2     2 BraA…  13.0   6.77 1714.      0     0 <NA>  <NA>     
 3     3 BraA…  12.8   6.55 5105.      0     0 <NA>  <NA>     
 4     4 BraA…  12.6   7.57 2909.      0     0 AT2G… <NA>     
 5     5 BraA… -12.0   6.43 5449.      0     0 <NA>  <NA>     
 6     6 BraA… -11.8   7.08 3622.      0     0 AT3G… <NA>     
 7     7 BraA…  11.7   5.50 3920.      0     0 <NA>  <NA>     
 8     8 BraA…  11.7   5.49 3480.      0     0 <NA>  <NA>     
 9     9 BraA…  11.7   6.18 3861.      0     0 AT5G… <NA>     
10    10 BraA…  11.6   5.36 2391.      0     0 <NA>  <NA>     
# ... with 18,979 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.genotypeFPsc.DEGs.add.rD.rR500.v3.0anno
# A tibble: 18,989 x 11
      X1 genes logFC logCPM    LR PValue   FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>  <dbl> <dbl> <chr> <chr>    
 1     1 BraA… -13.4   7.50 3038.      0     0 AT1G… <NA>     
 2     2 BraA…  13.0   6.77 1714.      0     0 <NA>  <NA>     
 3     3 BraA…  12.8   6.55 5105.      0     0 <NA>  <NA>     
 4     4 BraA…  12.6   7.57 2909.      0     0 AT2G… <NA>     
 5     5 BraA… -12.0   6.43 5449.      0     0 <NA>  <NA>     
 6     6 BraA… -11.8   7.08 3622.      0     0 AT3G… <NA>     
 7     7 BraA…  11.7   5.50 3920.      0     0 <NA>  <NA>     
 8     8 BraA…  11.7   5.49 3480.      0     0 <NA>  <NA>     
 9     9 BraA…  11.7   6.18 3861.      0     0 AT5G… <NA>     
10    10 BraA…  11.6   5.36 2391.      0     0 <NA>  <NA>     
# ... with 18,979 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.genotypeR500_trt5E_live.genotypeR500_trt5E_dead.genotypeR500.DEGs.int.rB.rFPsc.v3.0anno
# A tibble: 17,373 x 13
      X1 genes logFC.genotypeR… logFC.genotypeR… logFC.genotypeR… logCPM
   <int> <chr>            <dbl>            <dbl>            <dbl>  <dbl>
 1     1 BraA…            -14.4           2.48             2.08     7.57
 2     2 BraA…             14.3          -1.08            -1.42     7.50
 3     3 BraA…            -13.6           1.30             0.0224   6.77
 4     4 BraA…            -13.0           1.33             1.99     6.18
 5     5 BraA…             12.6          -2.16            -2.96     5.81
 6     6 BraA…            -12.5           4.21             4.13     5.83
 7     7 BraA…            -12.3           0.131            1.29     5.50
 8     8 BraA…            -12.3           1.42             0.269    5.36
 9     9 BraA…            -12.2          -0.0831           1.14     5.49
10    10 BraA…            -12.1           0.139            2.13     5.21
# ... with 17,363 more rows, and 7 more variables: LR <dbl>, PValue <dbl>,
#   FDR <dbl>, AGI <chr>, At_symbol <chr>, At_short_description <chr>,
#   perc_ID <dbl>

$root.genotypeR500_trt5E_live.genotypeR500_trtBLANK_NA.genotypeR500.DEGs.int.rD.rFPsc.v3.0anno
# A tibble: 17,373 x 13
      X1 genes logFC.genotypeR… logFC.genotypeR… logFC.genotypeR… logCPM
   <int> <chr>            <dbl>            <dbl>            <dbl>  <dbl>
 1     1 BraA…            -13.3           1.28            -0.0181   6.55
 2     2 BraA…             13.2           1.08            -0.338    7.50
 3     3 BraA…             13.2          -1.76            -1.23     6.43
 4     4 BraA…             12.5          -0.465           -1.32     7.08
 5     5 BraA…            -12.3           0.0831           1.22     5.49
 6     6 BraA…            -12.2          -1.30            -1.28     6.77
 7     7 BraA…            -12.2          -0.131            1.16     5.50
 8     8 BraA…             12.0          -1.24            -1.70     5.33
 9     9 BraA…            -12.0          -0.139            1.99     5.21
10    10 BraA…            -11.9          -2.48            -0.395    7.57
# ... with 17,363 more rows, and 7 more variables: LR <dbl>, PValue <dbl>,
#   FDR <dbl>, AGI <chr>, At_symbol <chr>, At_short_description <chr>,
#   perc_ID <dbl>

$root.genotypeR500.DEGs.add.rB.rFPsc.v3.0anno
# A tibble: 18,989 x 11
      X1 genes logFC logCPM    LR PValue   FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>  <dbl> <dbl> <chr> <chr>    
 1     1 BraA…  13.4   7.50 3038.      0     0 AT1G… <NA>     
 2     2 BraA… -13.0   6.77 1714.      0     0 <NA>  <NA>     
 3     3 BraA… -12.8   6.55 5105.      0     0 <NA>  <NA>     
 4     4 BraA… -12.6   7.57 2909.      0     0 AT2G… <NA>     
 5     5 BraA…  12.0   6.43 5449.      0     0 <NA>  <NA>     
 6     6 BraA…  11.8   7.08 3622.      0     0 AT3G… <NA>     
 7     7 BraA… -11.7   5.50 3920.      0     0 <NA>  <NA>     
 8     8 BraA… -11.7   5.49 3480.      0     0 <NA>  <NA>     
 9     9 BraA… -11.7   6.18 3861.      0     0 AT5G… <NA>     
10    10 BraA… -11.6   5.36 2391.      0     0 <NA>  <NA>     
# ... with 18,979 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.genotypeR500.DEGs.add.rD.rFPsc.v3.0anno
# A tibble: 18,989 x 11
      X1 genes logFC logCPM    LR PValue   FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>  <dbl> <dbl> <chr> <chr>    
 1     1 BraA…  13.4   7.50 3038.      0     0 AT1G… <NA>     
 2     2 BraA… -13.0   6.77 1714.      0     0 <NA>  <NA>     
 3     3 BraA… -12.8   6.55 5105.      0     0 <NA>  <NA>     
 4     4 BraA… -12.6   7.57 2909.      0     0 AT2G… <NA>     
 5     5 BraA…  12.0   6.43 5449.      0     0 <NA>  <NA>     
 6     6 BraA…  11.8   7.08 3622.      0     0 AT3G… <NA>     
 7     7 BraA… -11.7   5.50 3920.      0     0 <NA>  <NA>     
 8     8 BraA… -11.7   5.49 3480.      0     0 <NA>  <NA>     
 9     9 BraA… -11.7   6.18 3861.      0     0 AT5G… <NA>     
10    10 BraA… -11.6   5.36 2391.      0     0 <NA>  <NA>     
# ... with 18,979 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.R500.trtlive.DEGs.all.rD.v3.0anno
# A tibble: 383 x 11
      X1 genes  logFC logCPM    LR  PValue     FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>   <dbl>   <dbl> <chr> <chr>    
 1     1 BraA…  1.26    4.60  33.9 5.82e-9 1.55e-4 AT1G… NLP4     
 2     2 BraA…  2.13    3.39  32.5 1.20e-8 1.60e-4 AT1G… <NA>     
 3     3 BraA…  2.23    1.67  31.4 2.05e-8 1.83e-4 AT3G… ABCA3    
 4     4 BraA…  1.70    3.81  30.6 3.14e-8 1.93e-4 AT3G… NF-YA6   
 5     5 BraA… -1.53    4.64  30.3 3.61e-8 1.93e-4 AT4G… <NA>     
 6     6 BraA…  1.28    3.98  29.2 6.42e-8 2.86e-4 AT5G… GLN1;4   
 7     7 BraA… -1.14    5.84  28.4 1.00e-7 3.29e-4 AT1G… AtNIGT1  
 8     8 BraA…  0.988   5.18  28.2 1.09e-7 3.29e-4 AT5G… <NA>     
 9     9 BraA…  1.77    5.64  28.2 1.12e-7 3.29e-4 AT5G… ATDUR3   
10    10 BraA… -1.37    3.74  27.9 1.30e-7 3.29e-4 AT1G… AtNIGT1  
# ... with 373 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.trt5E_dead.DEGs.add.rB.rFPsc.v3.0anno
# A tibble: 23 x 11
      X1 genes  logFC  logCPM    LR  PValue     FDR AGI   At_symbol
   <int> <chr>  <dbl>   <dbl> <dbl>   <dbl>   <dbl> <chr> <chr>    
 1     1 BraA…  1.42   2.28    32.0 1.53e-8 4.27e-4 AT5G… <NA>     
 2     2 BraA…  1.99   1.62    26.6 2.46e-7 3.43e-3 AT4G… CYP82C4  
 3     3 BraA…  0.941  2.67    24.2 8.86e-7 7.05e-3 AT3G… <NA>     
 4     4 BraA…  1.81   1.53    23.9 1.01e-6 7.05e-3 AT4G… ATIRT1   
 5     5 BraA…  1.67   0.0566  20.8 5.15e-6 2.73e-2 AT1G… <NA>     
 6     6 BraA…  1.43   0.469   20.5 5.87e-6 2.73e-2 AT2G… Iqd4     
 7     7 BraA…  1.42   2.16    19.9 8.24e-6 3.28e-2 AT2G… <NA>     
 8     8 BraA…  1.45   3.39    19.5 1.02e-5 3.28e-2 AT5G… <NA>     
 9     9 BraA…  1.47   2.36    19.2 1.16e-5 3.28e-2 AT5G… ATPT4    
10    10 BraA… -4.78  -0.507   19.1 1.26e-5 3.28e-2 <NA>  <NA>     
# ... with 13 more rows, and 2 more variables: At_short_description <chr>,
#   perc_ID <dbl>

$root.trt5E_dead.DEGs.add.rB.rR500.v3.0anno
# A tibble: 23 x 11
      X1 genes  logFC  logCPM    LR  PValue     FDR AGI   At_symbol
   <int> <chr>  <dbl>   <dbl> <dbl>   <dbl>   <dbl> <chr> <chr>    
 1     1 BraA…  1.42   2.28    32.0 1.53e-8 4.27e-4 AT5G… <NA>     
 2     2 BraA…  1.99   1.62    26.6 2.46e-7 3.43e-3 AT4G… CYP82C4  
 3     3 BraA…  0.941  2.67    24.2 8.86e-7 7.05e-3 AT3G… <NA>     
 4     4 BraA…  1.81   1.53    23.9 1.01e-6 7.05e-3 AT4G… ATIRT1   
 5     5 BraA…  1.67   0.0566  20.8 5.15e-6 2.73e-2 AT1G… <NA>     
 6     6 BraA…  1.43   0.469   20.5 5.87e-6 2.73e-2 AT2G… Iqd4     
 7     7 BraA…  1.42   2.16    19.9 8.24e-6 3.28e-2 AT2G… <NA>     
 8     8 BraA…  1.45   3.39    19.5 1.02e-5 3.28e-2 AT5G… <NA>     
 9     9 BraA…  1.47   2.36    19.2 1.16e-5 3.28e-2 AT5G… ATPT4    
10    10 BraA… -4.78  -0.507   19.1 1.26e-5 3.28e-2 <NA>  <NA>     
# ... with 13 more rows, and 2 more variables: At_short_description <chr>,
#   perc_ID <dbl>

$root.trt5E_dead.genotypeFPsc_trt5E_dead.DEGs.int.rB.rR500.v3.0anno
# A tibble: 40 x 12
      X1 genes logFC.trt5E_dead logFC.genotypeF… logCPM    LR  PValue
   <int> <chr>            <dbl>            <dbl>  <dbl> <dbl>   <dbl>
 1     1 BraA…          -0.0755           2.15    6.68   39.4 2.73e-9
 2     2 BraA…           0.797            1.55    1.62   37.3 8.04e-9
 3     3 BraA…           1.41             0.0163  2.28   30.9 1.99e-7
 4     4 BraA…           0.882            1.65    1.59   28.4 6.96e-7
 5     5 BraA…           0.770            1.39    3.39   27.0 1.38e-6
 6     6 BraA…          -0.174            1.33    2.87   26.4 1.82e-6
 7     7 BraA…          -0.0525          -3.86    2.45   26.3 1.93e-6
 8     8 BraA…           0.143            2.27    2.81   24.9 3.94e-6
 9     9 BraA…           0.901            1.15    0.469  24.2 5.61e-6
10    10 BraA…           0.0770           1.36    9.03   23.6 7.66e-6
# ... with 30 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$root.trt5E_dead.genotypeR500_trt5E_dead.DEGs.int.rB.rFPsc.v3.0anno
# A tibble: 40 x 12
      X1 genes logFC.trt5E_dead logFC.genotypeR… logCPM    LR  PValue
   <int> <chr>            <dbl>            <dbl>  <dbl> <dbl>   <dbl>
 1     1 BraA…             2.07          -2.15    6.68   39.4 2.73e-9
 2     2 BraA…             2.35          -1.55    1.62   37.3 8.04e-9
 3     3 BraA…             1.42          -0.0163  2.28   30.9 1.99e-7
 4     4 BraA…             2.53          -1.65    1.59   28.4 6.96e-7
 5     5 BraA…             2.16          -1.39    3.39   27.0 1.38e-6
 6     6 BraA…             1.16          -1.33    2.87   26.4 1.82e-6
 7     7 BraA…            -3.92           3.86    2.45   26.3 1.93e-6
 8     8 BraA…             2.41          -2.27    2.81   24.9 3.94e-6
 9     9 BraA…             2.06          -1.15    0.469  24.2 5.61e-6
10    10 BraA…             1.44          -1.36    9.03   23.6 7.66e-6
# ... with 30 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$root.trt5E_live.DEGs.add.rB.rFPsc.v3.0anno
# A tibble: 931 x 11
      X1 genes  logFC logCPM    LR   PValue     FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>    <dbl>   <dbl> <chr> <chr>    
 1     1 BraA… -1.28   2.79   48.3 3.58e-12 9.97e-8 AT2G… <NA>     
 2     2 BraA… -0.853  7.44   39.7 2.94e-10 4.10e-6 AT3G… AtDJ1A   
 3     3 BraA… -1.01   5.65   38.3 6.09e-10 5.66e-6 AT1G… AtNIGT1  
 4     4 BraA… -0.728  6.87   36.3 1.71e- 9 1.19e-5 AT3G… AtDJ1A   
 5     5 BraA…  1.11   3.16   33.4 7.41e- 9 4.13e-5 AT4G… AAT1     
 6     6 BraA…  2.09   1.69   32.9 9.58e- 9 4.45e-5 AT1G… PHT1;8   
 7     7 BraA…  1.41   0.714  30.2 3.96e- 8 1.58e-4 AT1G… <NA>     
 8     8 BraA…  1.30   2.16   29.4 5.96e- 8 2.08e-4 AT5G… AtMYB19  
 9     9 BraA…  1.12   1.66   28.4 9.71e- 8 2.49e-4 AT4G… <NA>     
10    10 BraA…  1.23   3.30   28.3 1.02e- 7 2.49e-4 AT3G… LAC7     
# ... with 921 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.trt5E_live.DEGs.add.rB.rR500.v3.0anno
# A tibble: 931 x 11
      X1 genes  logFC logCPM    LR   PValue     FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>    <dbl>   <dbl> <chr> <chr>    
 1     1 BraA… -1.28   2.79   48.3 3.58e-12 9.97e-8 AT2G… <NA>     
 2     2 BraA… -0.853  7.44   39.7 2.94e-10 4.10e-6 AT3G… AtDJ1A   
 3     3 BraA… -1.01   5.65   38.3 6.09e-10 5.66e-6 AT1G… AtNIGT1  
 4     4 BraA… -0.728  6.87   36.3 1.71e- 9 1.19e-5 AT3G… AtDJ1A   
 5     5 BraA…  1.11   3.16   33.4 7.41e- 9 4.13e-5 AT4G… AAT1     
 6     6 BraA…  2.09   1.69   32.9 9.58e- 9 4.45e-5 AT1G… PHT1;8   
 7     7 BraA…  1.41   0.714  30.2 3.96e- 8 1.58e-4 AT1G… <NA>     
 8     8 BraA…  1.30   2.16   29.4 5.96e- 8 2.08e-4 AT5G… AtMYB19  
 9     9 BraA…  1.12   1.66   28.4 9.71e- 8 2.49e-4 AT4G… <NA>     
10    10 BraA…  1.23   3.30   28.3 1.02e- 7 2.49e-4 AT3G… LAC7     
# ... with 921 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.trt5E_live.DEGs.add.rD.rFPsc.v3.0anno
# A tibble: 26 x 11
      X1 genes  logFC logCPM    LR  PValue     FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>   <dbl>   <dbl> <chr> <chr>    
 1     1 BraA… -1.37    2.49  35.6 2.39e-9 6.66e-5 AT3G… BHLH039  
 2     2 BraA… -1.38    1.82  31.6 1.93e-8 2.20e-4 AT3G… BHLH039  
 3     3 BraA… -0.754   7.44  31.2 2.37e-8 2.20e-4 AT3G… AtDJ1A   
 4     4 BraA… -0.648   6.87  28.8 7.97e-8 5.56e-4 AT3G… AtDJ1A   
 5     5 BraA… -0.600   5.31  27.9 1.30e-7 7.24e-4 AT4G… UGT73B1  
 6     6 BraA… -0.616   5.60  27.0 2.02e-7 9.37e-4 AT4G… UGT73B1  
 7     7 BraA…  1.21    2.58  26.2 3.10e-7 1.04e-3 AT1G… TAR4     
 8     8 BraA… -0.831   5.65  26.1 3.26e-7 1.04e-3 AT1G… AtNIGT1  
 9     9 BraA…  1.69    3.06  26.0 3.37e-7 1.04e-3 AT1G… <NA>     
10    10 BraA… -1.10    7.15  24.8 6.25e-7 1.74e-3 AT1G… <NA>     
# ... with 16 more rows, and 2 more variables: At_short_description <chr>,
#   perc_ID <dbl>

$root.trt5E_live.DEGs.add.rD.rR500.v3.0anno
# A tibble: 26 x 11
      X1 genes  logFC logCPM    LR  PValue     FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>   <dbl>   <dbl> <chr> <chr>    
 1     1 BraA… -1.37    2.49  35.6 2.39e-9 6.66e-5 AT3G… BHLH039  
 2     2 BraA… -1.38    1.82  31.6 1.93e-8 2.20e-4 AT3G… BHLH039  
 3     3 BraA… -0.754   7.44  31.2 2.37e-8 2.20e-4 AT3G… AtDJ1A   
 4     4 BraA… -0.648   6.87  28.8 7.97e-8 5.56e-4 AT3G… AtDJ1A   
 5     5 BraA… -0.600   5.31  27.9 1.30e-7 7.24e-4 AT4G… UGT73B1  
 6     6 BraA… -0.616   5.60  27.0 2.02e-7 9.37e-4 AT4G… UGT73B1  
 7     7 BraA…  1.21    2.58  26.2 3.10e-7 1.04e-3 AT1G… TAR4     
 8     8 BraA… -0.831   5.65  26.1 3.26e-7 1.04e-3 AT1G… AtNIGT1  
 9     9 BraA…  1.69    3.06  26.0 3.37e-7 1.04e-3 AT1G… <NA>     
10    10 BraA… -1.10    7.15  24.8 6.25e-7 1.74e-3 AT1G… <NA>     
# ... with 16 more rows, and 2 more variables: At_short_description <chr>,
#   perc_ID <dbl>

$root.trt5E_live.genotypeFPsc_trt5E_live.DEGs.int.rB.rR500.v3.0anno
# A tibble: 608 x 12
      X1 genes logFC.trt5E_live logFC.genotypeF… logCPM    LR   PValue
   <int> <chr>            <dbl>            <dbl>  <dbl> <dbl>    <dbl>
 1     1 BraA…           -1.45             0.859   5.65  53.8 2.04e-12
 2     2 BraA…           -1.55             0.526   2.79  53.2 2.87e-12
 3     3 BraA…           -0.697           -1.05    7.15  44.3 2.45e-10
 4     4 BraA…           -0.663           -0.389   7.44  42.9 4.75e-10
 5     5 BraA…           -0.556           -0.349   6.87  38.8 3.76e- 9
 6     6 BraA…            1.06             1.83    1.59  38.6 4.18e- 9
 7     7 BraA…            1.73            -0.931   2.16  38.6 4.25e- 9
 8     8 BraA…            0.900            0.654   3.16  37.9 5.79e- 9
 9     9 BraA…            0.946            1.34    5.01  36.4 1.23e- 8
10    10 BraA…            0.527            0.753   4.69  35.9 1.61e- 8
# ... with 598 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$root.trt5E_live.genotypeFPsc_trt5E_live.DEGs.int.rD.rR500.v3.0anno
# A tibble: 77 x 12
      X1 genes logFC.trt5E_live logFC.genotypeF… logCPM    LR   PValue
   <int> <chr>            <dbl>            <dbl>  <dbl> <dbl>    <dbl>
 1     1 BraA…           -0.538           -1.21   7.15   41.7 8.66e-10
 2     2 BraA…           -1.14             0.590  5.65   35.9 1.59e- 8
 3     3 BraA…           -1.50             0.191  2.49   35.1 2.43e- 8
 4     4 BraA…           -0.581           -0.358  7.44   33.9 4.30e- 8
 5     5 BraA…            2.22            -2.33   1.23   33.7 4.91e- 8
 6     6 BraA…            1.57            -1.36   4.01   31.8 1.26e- 7
 7     7 BraA…           -0.836           -1.91   0.848  31.7 1.32e- 7
 8     8 BraA…           -1.58             0.333  1.82   31.2 1.66e- 7
 9     9 BraA…           -0.529           -0.246  6.87   30.4 2.55e- 7
10    10 BraA…            1.69            -1.46   3.49   29.9 3.29e- 7
# ... with 67 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$root.trt5E_live.genotypeFPsc.DEGs.int.rB.rR500.v3.0anno
# A tibble: 4 x 11
     X1 genes logFC logCPM    LR  PValue     FDR AGI   At_symbol
  <int> <chr> <dbl>  <dbl> <dbl>   <dbl>   <dbl> <chr> <chr>    
1     1 BraA… -4.86  4.91   25.7 3.90e-7 0.00548 AT1G… ATU2AF65B
2     2 BraA…  3.42  0.428  25.7 3.93e-7 0.00548 AT5G… <NA>     
3     3 BraA… -1.55  1.93   20.4 6.29e-6 0.0453  AT4G… UBC17    
4     4 BraA…  2.02  6.68   20.3 6.50e-6 0.0453  AT4G… <NA>     
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>

$root.trt5E_live.genotypeFPsc.DEGs.int.rD.rR500.v3.0anno
# A tibble: 2 x 11
     X1 genes logFC logCPM    LR  PValue    FDR AGI   At_symbol
  <int> <chr> <dbl>  <dbl> <dbl>   <dbl>  <dbl> <chr> <chr>    
1     1 BraA…  3.28  1.39   23.8 1.05e-6 0.0293 AT3G… <NA>     
2     2 BraA…  2.95  0.428  21.5 3.55e-6 0.0495 AT5G… <NA>     
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>

$root.trt5E_live.genotypeR500_trt5E_live.DEGs.int.rB.rFPsc.v3.0anno
# A tibble: 608 x 12
      X1 genes logFC.trt5E_live logFC.genotypeR… logCPM    LR   PValue
   <int> <chr>            <dbl>            <dbl>  <dbl> <dbl>    <dbl>
 1     1 BraA…           -0.590           -0.859   5.65  53.8 2.04e-12
 2     2 BraA…           -1.03            -0.526   2.79  53.2 2.87e-12
 3     3 BraA…           -1.74             1.05    7.15  44.3 2.45e-10
 4     4 BraA…           -1.05             0.389   7.44  42.9 4.75e-10
 5     5 BraA…           -0.905            0.349   6.87  38.8 3.76e- 9
 6     6 BraA…            2.89            -1.83    1.59  38.6 4.18e- 9
 7     7 BraA…            0.799            0.931   2.16  38.6 4.25e- 9
 8     8 BraA…            1.55            -0.654   3.16  37.9 5.79e- 9
 9     9 BraA…            2.29            -1.34    5.01  36.4 1.23e- 8
10    10 BraA…            1.28            -0.753   4.69  35.9 1.61e- 8
# ... with 598 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$root.trt5E_live.genotypeR500_trt5E_live.DEGs.int.rD.rFPsc.v3.0anno
# A tibble: 77 x 12
      X1 genes logFC.trt5E_live logFC.genotypeR… logCPM    LR   PValue
   <int> <chr>            <dbl>            <dbl>  <dbl> <dbl>    <dbl>
 1     1 BraA…           -1.75             1.21   7.15   41.7 8.66e-10
 2     2 BraA…           -0.554           -0.590  5.65   35.9 1.59e- 8
 3     3 BraA…           -1.31            -0.191  2.49   35.1 2.43e- 8
 4     4 BraA…           -0.939            0.358  7.44   33.9 4.30e- 8
 5     5 BraA…           -0.113            2.33   1.23   33.7 4.91e- 8
 6     6 BraA…            0.211            1.36   4.01   31.8 1.26e- 7
 7     7 BraA…           -2.75             1.91   0.848  31.7 1.32e- 7
 8     8 BraA…           -1.25            -0.333  1.82   31.2 1.66e- 7
 9     9 BraA…           -0.775            0.246  6.87   30.4 2.55e- 7
10    10 BraA…            0.236            1.46   3.49   29.9 3.29e- 7
# ... with 67 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$root.trt5E_live.genotypeR500.DEGs.int.rB.rFPsc.v3.0anno
# A tibble: 4 x 11
     X1 genes logFC logCPM    LR  PValue     FDR AGI   At_symbol
  <int> <chr> <dbl>  <dbl> <dbl>   <dbl>   <dbl> <chr> <chr>    
1     1 BraA…  4.86  4.91   25.7 3.90e-7 0.00548 AT1G… ATU2AF65B
2     2 BraA… -3.42  0.428  25.7 3.93e-7 0.00548 AT5G… <NA>     
3     3 BraA…  1.55  1.93   20.4 6.29e-6 0.0453  AT4G… UBC17    
4     4 BraA… -2.02  6.68   20.3 6.50e-6 0.0453  AT4G… <NA>     
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>
# confirm
DEG.count.list.e1.v3.0annotation.all.FDR0.05[["root.R500.trtlive.DEGs.all.rD.v3.0anno"]] %>% View() # OK. 383 genes

# Reading DEGs list exp3

# all model including subset data
DEG.objs.e3.v3.0annotation.all<-list.files(path=file.path("..","v3.0annotation","20180202-samples","output","FULLtoptag"),
           pattern="(^leaf|^root)(\\.)(.+)(v3.0anno)(.csv)") 
# read csv file (only full model)
DEG.count.list.e3.v3.0annotation.all<-lapply(DEG.objs.e3.v3.0annotation.all, function(x) read_csv(paste(file.path("..","v3.0annotation","20180202-samples","output","FULLtoptag"),"/",x,sep="")))
names(DEG.count.list.e3.v3.0annotation.all)<-gsub(".csv","",DEG.objs.e3.v3.0annotation.all)
DEG.count.list.e3.v3.0annotation.all[["root.cr.trtlive.DEGs.all.rD.v3.0anno"]] %>% filter(FDR<0.05)
# A tibble: 3,887 x 11
      X1 genes  logFC logCPM    LR   PValue      FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>    <dbl>    <dbl> <chr> <chr>    
 1     1 BraA… -1.96    4.70  87.7 7.54e-21 1.07e-16 AT1G… ASP4     
 2     2 BraA…  1.22    5.63  87.6 8.17e-21 1.07e-16 AT2G… <NA>     
 3     3 BraA…  1.28    5.28  83.6 6.07e-20 5.29e-16 AT1G… BRR2     
 4     4 BraA… -1.15    5.99  81.6 1.70e-19 1.11e-15 AT2G… <NA>     
 5     5 BraA…  1.14    7.09  75.2 4.17e-18 2.18e-14 AT1G… BRR2     
 6     6 BraA…  1.02    5.44  74.1 7.24e-18 3.16e-14 AT5G… <NA>     
 7     7 BraA…  1.94    3.77  71.4 2.91e-17 1.09e-13 AT3G… TIC      
 8     8 BraA…  0.928   7.49  69.8 6.47e-17 2.03e-13 AT2G… ATGSL03  
 9     9 BraA…  1.59    3.73  69.7 6.98e-17 2.03e-13 AT1G… ASU1     
10    10 BraA…  1.30    3.72  66.9 2.79e-16 7.10e-13 AT5G… <NA>     
# ... with 3,877 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>
names(DEG.count.list.e3.v3.0annotation.all)
 [1] "leaf.cr.trtlive.DEGs.all.rD.v3.0anno"                     
 [2] "leaf.densitycr_densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno"
 [3] "leaf.densitycr_densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno"
 [4] "leaf.densitycr.DEGs.add.rD.rUN.v3.0anno"                  
 [5] "leaf.densitycr.DEGs.add.rL.rUN.v3.0anno"                  
 [6] "leaf.densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno"          
 [7] "leaf.densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno"          
 [8] "leaf.densityun_densityun.trtdead.DEGs.int.rL.rCR.v3.0anno"
 [9] "leaf.densityun_densityun.trtlive.DEGs.int.rD.rCR.v3.0anno"
[10] "leaf.densityun.DEGs.add.rD.rCR.v3.0anno"                  
[11] "leaf.densityun.DEGs.add.rL.rCR.v3.0anno"                  
[12] "leaf.densityun.trtdead.DEGs.int.rL.rCR.v3.0anno"          
[13] "leaf.densityun.trtlive.DEGs.int.rD.rCR.v3.0anno"          
[14] "leaf.trtdead_densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno"  
[15] "leaf.trtdead_densityun.trtdead.DEGs.int.rL.rCR.v3.0anno"  
[16] "leaf.trtdead.DEGs.add.rL.rCR.v3.0anno"                    
[17] "leaf.trtdead.DEGs.add.rL.rUN.v3.0anno"                    
[18] "leaf.trtdead.DEGs.int.rL.rCR.v3.0anno"                    
[19] "leaf.trtdead.DEGs.int.rL.rUN.v3.0anno"                    
[20] "leaf.trtlive_densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno"  
[21] "leaf.trtlive_densityun.trtlive.DEGs.int.rD.rCR.v3.0anno"  
[22] "leaf.trtlive.DEGs.add.rD.rCR.v3.0anno"                    
[23] "leaf.trtlive.DEGs.add.rD.rUN.v3.0anno"                    
[24] "leaf.trtlive.DEGs.int.rD.rCR.v3.0anno"                    
[25] "leaf.trtlive.DEGs.int.rD.rUN.v3.0anno"                    
[26] "leaf.un.trtlive.DEGs.all.rD.v3.0anno"                     
[27] "root.cr.trtlive.DEGs.all.rD.v3.0anno"                     
[28] "root.densitycr_densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno"
[29] "root.densitycr_densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno"
[30] "root.densitycr.DEGs.add.rD.rUN.v3.0anno"                  
[31] "root.densitycr.DEGs.add.rL.rUN.v3.0anno"                  
[32] "root.densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno"          
[33] "root.densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno"          
[34] "root.densityun_densityun.trtdead.DEGs.int.rL.rCR.v3.0anno"
[35] "root.densityun_densityun.trtlive.DEGs.int.rD.rCR.v3.0anno"
[36] "root.densityun.DEGs.add.rD.rCR.v3.0anno"                  
[37] "root.densityun.DEGs.add.rL.rCR.v3.0anno"                  
[38] "root.densityun.trtdead.DEGs.int.rL.rCR.v3.0anno"          
[39] "root.densityun.trtlive.DEGs.int.rD.rCR.v3.0anno"          
[40] "root.trtdead_densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno"  
[41] "root.trtdead_densityun.trtdead.DEGs.int.rL.rCR.v3.0anno"  
[42] "root.trtdead.DEGs.add.rL.rCR.v3.0anno"                    
[43] "root.trtdead.DEGs.add.rL.rUN.v3.0anno"                    
[44] "root.trtdead.DEGs.int.rL.rCR.v3.0anno"                    
[45] "root.trtdead.DEGs.int.rL.rUN.v3.0anno"                    
[46] "root.trtlive_densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno"  
[47] "root.trtlive_densityun.trtlive.DEGs.int.rD.rCR.v3.0anno"  
[48] "root.trtlive.DEGs.add.rD.rCR.v3.0anno"                    
[49] "root.trtlive.DEGs.add.rD.rUN.v3.0anno"                    
[50] "root.trtlive.DEGs.int.rD.rCR.v3.0anno"                    
[51] "root.trtlive.DEGs.int.rD.rUN.v3.0anno"                    
[52] "root.un.trtlive.DEGs.all.rD.v3.0anno"                     
# FDR<0.05
DEG.count.list.e3.v3.0annotation.all %>% map(filter(FDR<0.05)) # does not work
Error in filter(FDR < 0.05): object 'FDR' not found
DEG.count.list.e3.v3.0annotation.all.FDR0.05<-DEG.count.list.e3.v3.0annotation.all %>% map(function(df) filter(df,FDR<0.05)) # does work
names(DEG.count.list.e3.v3.0annotation.all.FDR0.05)
 [1] "leaf.cr.trtlive.DEGs.all.rD.v3.0anno"                     
 [2] "leaf.densitycr_densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno"
 [3] "leaf.densitycr_densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno"
 [4] "leaf.densitycr.DEGs.add.rD.rUN.v3.0anno"                  
 [5] "leaf.densitycr.DEGs.add.rL.rUN.v3.0anno"                  
 [6] "leaf.densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno"          
 [7] "leaf.densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno"          
 [8] "leaf.densityun_densityun.trtdead.DEGs.int.rL.rCR.v3.0anno"
 [9] "leaf.densityun_densityun.trtlive.DEGs.int.rD.rCR.v3.0anno"
[10] "leaf.densityun.DEGs.add.rD.rCR.v3.0anno"                  
[11] "leaf.densityun.DEGs.add.rL.rCR.v3.0anno"                  
[12] "leaf.densityun.trtdead.DEGs.int.rL.rCR.v3.0anno"          
[13] "leaf.densityun.trtlive.DEGs.int.rD.rCR.v3.0anno"          
[14] "leaf.trtdead_densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno"  
[15] "leaf.trtdead_densityun.trtdead.DEGs.int.rL.rCR.v3.0anno"  
[16] "leaf.trtdead.DEGs.add.rL.rCR.v3.0anno"                    
[17] "leaf.trtdead.DEGs.add.rL.rUN.v3.0anno"                    
[18] "leaf.trtdead.DEGs.int.rL.rCR.v3.0anno"                    
[19] "leaf.trtdead.DEGs.int.rL.rUN.v3.0anno"                    
[20] "leaf.trtlive_densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno"  
[21] "leaf.trtlive_densityun.trtlive.DEGs.int.rD.rCR.v3.0anno"  
[22] "leaf.trtlive.DEGs.add.rD.rCR.v3.0anno"                    
[23] "leaf.trtlive.DEGs.add.rD.rUN.v3.0anno"                    
[24] "leaf.trtlive.DEGs.int.rD.rCR.v3.0anno"                    
[25] "leaf.trtlive.DEGs.int.rD.rUN.v3.0anno"                    
[26] "leaf.un.trtlive.DEGs.all.rD.v3.0anno"                     
[27] "root.cr.trtlive.DEGs.all.rD.v3.0anno"                     
[28] "root.densitycr_densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno"
[29] "root.densitycr_densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno"
[30] "root.densitycr.DEGs.add.rD.rUN.v3.0anno"                  
[31] "root.densitycr.DEGs.add.rL.rUN.v3.0anno"                  
[32] "root.densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno"          
[33] "root.densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno"          
[34] "root.densityun_densityun.trtdead.DEGs.int.rL.rCR.v3.0anno"
[35] "root.densityun_densityun.trtlive.DEGs.int.rD.rCR.v3.0anno"
[36] "root.densityun.DEGs.add.rD.rCR.v3.0anno"                  
[37] "root.densityun.DEGs.add.rL.rCR.v3.0anno"                  
[38] "root.densityun.trtdead.DEGs.int.rL.rCR.v3.0anno"          
[39] "root.densityun.trtlive.DEGs.int.rD.rCR.v3.0anno"          
[40] "root.trtdead_densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno"  
[41] "root.trtdead_densityun.trtdead.DEGs.int.rL.rCR.v3.0anno"  
[42] "root.trtdead.DEGs.add.rL.rCR.v3.0anno"                    
[43] "root.trtdead.DEGs.add.rL.rUN.v3.0anno"                    
[44] "root.trtdead.DEGs.int.rL.rCR.v3.0anno"                    
[45] "root.trtdead.DEGs.int.rL.rUN.v3.0anno"                    
[46] "root.trtlive_densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno"  
[47] "root.trtlive_densityun.trtlive.DEGs.int.rD.rCR.v3.0anno"  
[48] "root.trtlive.DEGs.add.rD.rCR.v3.0anno"                    
[49] "root.trtlive.DEGs.add.rD.rUN.v3.0anno"                    
[50] "root.trtlive.DEGs.int.rD.rCR.v3.0anno"                    
[51] "root.trtlive.DEGs.int.rD.rUN.v3.0anno"                    
[52] "root.un.trtlive.DEGs.all.rD.v3.0anno"                     
# alternative way
DEG.count.list.e3.v3.0annotation.all %>% map(~filter(.,FDR<0.05)) # does work
$leaf.cr.trtlive.DEGs.all.rD.v3.0anno
# A tibble: 12 x 11
      X1 genes  logFC logCPM    LR  PValue    FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>   <dbl>  <dbl> <chr> <chr>    
 1     1 BraA…  2.75   2.86   20.6 5.77e-6 0.0413 AT1G… <NA>     
 2     2 BraA…  1.05   8.17   19.2 1.19e-5 0.0413 AT5G… AtHsp90-3
 3     3 BraA… -3.07   0.296  18.7 1.49e-5 0.0413 AT2G… PLAT2    
 4     4 BraA…  2.69   0.508  18.7 1.50e-5 0.0413 AT1G… <NA>     
 5     5 BraA… -0.961  7.30   18.7 1.51e-5 0.0413 AT1G… AtPMT3   
 6     6 BraA…  1.64   3.71   18.7 1.51e-5 0.0413 AT5G… AAP4     
 7     7 BraA…  1.66   2.15   18.7 1.54e-5 0.0413 AT2G… ArathEUL…
 8     8 BraA… -0.846  4.97   18.5 1.71e-5 0.0413 AT4G… ATCAD7   
 9     9 BraA…  1.68   3.95   18.3 1.89e-5 0.0413 AT5G… <NA>     
10    10 BraA…  2.83   1.000  18.3 1.91e-5 0.0413 AT5G… ANAC092  
11    11 BraA…  2.35   2.04   18.2 1.94e-5 0.0413 AT5G… <NA>     
12    12 BraA…  1.67   2.20   17.8 2.40e-5 0.0469 AT5G… <NA>     
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>

$leaf.densitycr_densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno
# A tibble: 14,074 x 12
      X1 genes logFC.densitycr logFC.densitycr… logCPM    LR    PValue
   <int> <chr>           <dbl>            <dbl>  <dbl> <dbl>     <dbl>
 1     1 BraA…           -7.74          1.09      4.09  891. 2.88e-194
 2     2 BraA…           -2.65          0.0205    8.15  664. 7.63e-145
 3     3 BraA…           -2.66         -0.00762   7.37  574. 1.78e-125
 4     4 BraA…            3.98          0.267     7.24  510. 1.56e-111
 5     5 BraA…           -4.47          0.399     7.29  494. 6.31e-108
 6     6 BraA…           -2.65          0.139     7.53  491. 1.88e-107
 7     7 BraA…           -2.11         -0.281     6.87  477. 2.91e-104
 8     8 BraA…           -3.09          0.124     5.97  471. 5.85e-103
 9     9 BraA…           -3.07         -0.179     7.57  470. 7.61e-103
10    10 BraA…           -2.45         -0.0962    4.91  467. 3.40e-102
# ... with 14,064 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$leaf.densitycr_densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno
# A tibble: 14,074 x 12
      X1 genes logFC.densitycr logFC.densitycr… logCPM    LR    PValue
   <int> <chr>           <dbl>            <dbl>  <dbl> <dbl>     <dbl>
 1     1 BraA…           -6.65         -1.09      4.09  891. 2.88e-194
 2     2 BraA…           -2.63         -0.0205    8.15  664. 7.63e-145
 3     3 BraA…           -2.67          0.00762   7.37  574. 1.78e-125
 4     4 BraA…            4.25         -0.267     7.24  510. 1.56e-111
 5     5 BraA…           -4.07         -0.399     7.29  494. 6.31e-108
 6     6 BraA…           -2.51         -0.139     7.53  491. 1.88e-107
 7     7 BraA…           -2.39          0.281     6.87  477. 2.91e-104
 8     8 BraA…           -2.97         -0.124     5.97  471. 5.85e-103
 9     9 BraA…           -3.25          0.179     7.57  470. 7.61e-103
10    10 BraA…           -2.55          0.0962    4.91  467. 3.40e-102
# ... with 14,064 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$leaf.densitycr.DEGs.add.rD.rUN.v3.0anno
# A tibble: 14,919 x 11
      X1 genes logFC logCPM    LR    PValue       FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>     <dbl>     <dbl> <chr> <chr>    
 1     1 BraA… -7.03   4.09  860. 5.16e-189 1.23e-184 AT1G… ARR4     
 2     2 BraA… -2.64   8.15  678. 1.81e-149 2.16e-145 AT5G… RPL4     
 3     3 BraA… -2.67   7.37  588. 6.29e-130 5.01e-126 AT1G… ARP1     
 4     4 BraA…  4.11   7.24  512. 2.09e-113 1.25e-109 AT5G… <NA>     
 5     5 BraA… -2.58   7.53  497. 3.90e-110 1.86e-106 AT4G… HLN      
 6     6 BraA… -4.26   7.29  485. 1.51e-107 6.00e-104 AT5G… ATHD2    
 7     7 BraA… -3.03   5.97  480. 1.91e-106 6.52e-103 AT3G… <NA>     
 8     8 BraA… -2.50   4.91  478. 6.82e-106 2.04e-102 AT2G… ASHR2    
 9     9 BraA… -3.16   7.57  475. 2.11e-105 5.60e-102 AT5G… ATHD2    
10    10 BraA… -2.25   6.87  460. 5.80e-102 1.39e- 98 AT5G… NAP1;3   
# ... with 14,909 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$leaf.densitycr.DEGs.add.rL.rUN.v3.0anno
# A tibble: 14,919 x 11
      X1 genes logFC logCPM    LR    PValue       FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>     <dbl>     <dbl> <chr> <chr>    
 1     1 BraA… -7.03   4.09  860. 5.16e-189 1.23e-184 AT1G… ARR4     
 2     2 BraA… -2.64   8.15  678. 1.81e-149 2.16e-145 AT5G… RPL4     
 3     3 BraA… -2.67   7.37  588. 6.29e-130 5.01e-126 AT1G… ARP1     
 4     4 BraA…  4.11   7.24  512. 2.09e-113 1.25e-109 AT5G… <NA>     
 5     5 BraA… -2.58   7.53  497. 3.90e-110 1.86e-106 AT4G… HLN      
 6     6 BraA… -4.26   7.29  485. 1.51e-107 6.00e-104 AT5G… ATHD2    
 7     7 BraA… -3.03   5.97  480. 1.91e-106 6.52e-103 AT3G… <NA>     
 8     8 BraA… -2.50   4.91  478. 6.82e-106 2.04e-102 AT2G… ASHR2    
 9     9 BraA… -3.16   7.57  475. 2.11e-105 5.60e-102 AT5G… ATHD2    
10    10 BraA… -2.25   6.87  460. 5.80e-102 1.39e- 98 AT5G… NAP1;3   
# ... with 14,909 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$leaf.densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno
# A tibble: 2 x 11
     X1 genes logFC logCPM    LR  PValue    FDR AGI   At_symbol
  <int> <chr> <dbl>  <dbl> <dbl>   <dbl>  <dbl> <chr> <chr>    
1     1 BraA… -2.00  4.58   22.9 1.69e-6 0.0271 AT1G… ARR7     
2     2 BraA… -3.95  0.659  22.3 2.27e-6 0.0271 AT1G… <NA>     
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>

$leaf.densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno
# A tibble: 2 x 11
     X1 genes logFC logCPM    LR  PValue    FDR AGI   At_symbol
  <int> <chr> <dbl>  <dbl> <dbl>   <dbl>  <dbl> <chr> <chr>    
1     1 BraA…  2.00  4.58   22.9 1.69e-6 0.0271 AT1G… ARR7     
2     2 BraA…  3.95  0.659  22.3 2.27e-6 0.0271 AT1G… <NA>     
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>

$leaf.densityun_densityun.trtdead.DEGs.int.rL.rCR.v3.0anno
# A tibble: 14,074 x 12
      X1 genes logFC.densityun logFC.densityun… logCPM    LR    PValue
   <int> <chr>           <dbl>            <dbl>  <dbl> <dbl>     <dbl>
 1     1 BraA…            7.74         -1.09      4.09  891. 2.88e-194
 2     2 BraA…            2.65         -0.0205    8.15  664. 7.63e-145
 3     3 BraA…            2.66          0.00762   7.37  574. 1.78e-125
 4     4 BraA…           -3.98         -0.267     7.24  510. 1.56e-111
 5     5 BraA…            4.47         -0.399     7.29  494. 6.31e-108
 6     6 BraA…            2.65         -0.139     7.53  491. 1.88e-107
 7     7 BraA…            2.11          0.281     6.87  477. 2.91e-104
 8     8 BraA…            3.09         -0.124     5.97  471. 5.85e-103
 9     9 BraA…            3.07          0.179     7.57  470. 7.61e-103
10    10 BraA…            2.45          0.0962    4.91  467. 3.40e-102
# ... with 14,064 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$leaf.densityun_densityun.trtlive.DEGs.int.rD.rCR.v3.0anno
# A tibble: 14,074 x 12
      X1 genes logFC.densityun logFC.densityun… logCPM    LR    PValue
   <int> <chr>           <dbl>            <dbl>  <dbl> <dbl>     <dbl>
 1     1 BraA…            6.65          1.09      4.09  891. 2.88e-194
 2     2 BraA…            2.63          0.0205    8.15  664. 7.63e-145
 3     3 BraA…            2.67         -0.00762   7.37  574. 1.78e-125
 4     4 BraA…           -4.25          0.267     7.24  510. 1.56e-111
 5     5 BraA…            4.07          0.399     7.29  494. 6.31e-108
 6     6 BraA…            2.51          0.139     7.53  491. 1.88e-107
 7     7 BraA…            2.39         -0.281     6.87  477. 2.91e-104
 8     8 BraA…            2.97          0.124     5.97  471. 5.85e-103
 9     9 BraA…            3.25         -0.179     7.57  470. 7.61e-103
10    10 BraA…            2.55         -0.0962    4.91  467. 3.40e-102
# ... with 14,064 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$leaf.densityun.DEGs.add.rD.rCR.v3.0anno
# A tibble: 14,919 x 11
      X1 genes logFC logCPM    LR    PValue       FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>     <dbl>     <dbl> <chr> <chr>    
 1     1 BraA…  7.03   4.09  860. 5.16e-189 1.23e-184 AT1G… ARR4     
 2     2 BraA…  2.64   8.15  678. 1.81e-149 2.16e-145 AT5G… RPL4     
 3     3 BraA…  2.67   7.37  588. 6.29e-130 5.01e-126 AT1G… ARP1     
 4     4 BraA… -4.11   7.24  512. 2.09e-113 1.25e-109 AT5G… <NA>     
 5     5 BraA…  2.58   7.53  497. 3.90e-110 1.86e-106 AT4G… HLN      
 6     6 BraA…  4.26   7.29  485. 1.51e-107 6.00e-104 AT5G… ATHD2    
 7     7 BraA…  3.03   5.97  480. 1.91e-106 6.52e-103 AT3G… <NA>     
 8     8 BraA…  2.50   4.91  478. 6.82e-106 2.04e-102 AT2G… ASHR2    
 9     9 BraA…  3.16   7.57  475. 2.11e-105 5.60e-102 AT5G… ATHD2    
10    10 BraA…  2.25   6.87  460. 5.80e-102 1.39e- 98 AT5G… NAP1;3   
# ... with 14,909 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$leaf.densityun.DEGs.add.rL.rCR.v3.0anno
# A tibble: 14,919 x 11
      X1 genes logFC logCPM    LR    PValue       FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>     <dbl>     <dbl> <chr> <chr>    
 1     1 BraA…  7.03   4.09  860. 5.16e-189 1.23e-184 AT1G… ARR4     
 2     2 BraA…  2.64   8.15  678. 1.81e-149 2.16e-145 AT5G… RPL4     
 3     3 BraA…  2.67   7.37  588. 6.29e-130 5.01e-126 AT1G… ARP1     
 4     4 BraA… -4.11   7.24  512. 2.09e-113 1.25e-109 AT5G… <NA>     
 5     5 BraA…  2.58   7.53  497. 3.90e-110 1.86e-106 AT4G… HLN      
 6     6 BraA…  4.26   7.29  485. 1.51e-107 6.00e-104 AT5G… ATHD2    
 7     7 BraA…  3.03   5.97  480. 1.91e-106 6.52e-103 AT3G… <NA>     
 8     8 BraA…  2.50   4.91  478. 6.82e-106 2.04e-102 AT2G… ASHR2    
 9     9 BraA…  3.16   7.57  475. 2.11e-105 5.60e-102 AT5G… ATHD2    
10    10 BraA…  2.25   6.87  460. 5.80e-102 1.39e- 98 AT5G… NAP1;3   
# ... with 14,909 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$leaf.densityun.trtdead.DEGs.int.rL.rCR.v3.0anno
# A tibble: 2 x 12
     X1 genes logFC logCPM    LR  PValue    FDR  X1_1 AGI   At_symbol
  <int> <chr> <dbl>  <dbl> <dbl>   <dbl>  <dbl> <int> <chr> <chr>    
1     1 BraA…  2.00  4.58   22.9 1.69e-6 0.0271 23774 AT1G… ARR7     
2     2 BraA…  3.95  0.659  22.3 2.27e-6 0.0271 33024 AT1G… <NA>     
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>

$leaf.densityun.trtlive.DEGs.int.rD.rCR.v3.0anno
# A tibble: 2 x 11
     X1 genes logFC logCPM    LR  PValue    FDR AGI   At_symbol
  <int> <chr> <dbl>  <dbl> <dbl>   <dbl>  <dbl> <chr> <chr>    
1     1 BraA… -2.00  4.58   22.9 1.69e-6 0.0271 AT1G… ARR7     
2     2 BraA… -3.95  0.659  22.3 2.27e-6 0.0271 AT1G… <NA>     
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>

$leaf.trtdead_densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno
# A tibble: 63 x 12
      X1 genes logFC.trtdead logFC.densitycr… logCPM    LR  PValue     FDR
   <int> <chr>         <dbl>            <dbl>  <dbl> <dbl>   <dbl>   <dbl>
 1     1 BraA…       -0.276            -0.766  7.58   29.4 4.09e-7 0.00976
 2     2 BraA…       -0.489            -0.376  4.13   26.8 1.54e-6 0.0177 
 3     3 BraA…        0.758             2.15   0.654  25.6 2.74e-6 0.0177 
 4     4 BraA…        0.189             0.714  4.94   25.2 3.36e-6 0.0177 
 5     5 BraA…       -0.0786           -1.22   5.52   24.7 4.23e-6 0.0177 
 6     6 BraA…        0.192             0.772  4.89   24.6 4.45e-6 0.0177 
 7     7 BraA…        0.124             1.14   4.46   24.1 5.93e-6 0.0186 
 8     8 BraA…        1.25             -3.95   0.659  23.9 6.59e-6 0.0186 
 9     9 BraA…        0.0242           -1.70   3.11   23.5 7.77e-6 0.0186 
10    10 BraA…        0.916            -2.00   4.58   23.5 7.80e-6 0.0186 
# ... with 53 more rows, and 4 more variables: AGI <chr>, At_symbol <chr>,
#   At_short_description <chr>, perc_ID <dbl>

$leaf.trtdead_densityun.trtdead.DEGs.int.rL.rCR.v3.0anno
# A tibble: 63 x 12
      X1 genes logFC.trtdead logFC.densityun… logCPM    LR  PValue     FDR
   <int> <chr>         <dbl>            <dbl>  <dbl> <dbl>   <dbl>   <dbl>
 1     1 BraA…        -1.04             0.766  7.58   29.4 4.09e-7 0.00976
 2     2 BraA…        -0.865            0.376  4.13   26.8 1.54e-6 0.0177 
 3     3 BraA…         2.90            -2.15   0.654  25.6 2.74e-6 0.0177 
 4     4 BraA…         0.903           -0.714  4.94   25.2 3.36e-6 0.0177 
 5     5 BraA…        -1.30             1.22   5.52   24.7 4.23e-6 0.0177 
 6     6 BraA…         0.964           -0.772  4.89   24.6 4.45e-6 0.0177 
 7     7 BraA…         1.27            -1.14   4.46   24.1 5.93e-6 0.0186 
 8     8 BraA…        -2.70             3.95   0.659  23.9 6.59e-6 0.0186 
 9     9 BraA…        -1.67             1.70   3.11   23.5 7.77e-6 0.0186 
10    10 BraA…        -1.09             2.00   4.58   23.5 7.80e-6 0.0186 
# ... with 53 more rows, and 4 more variables: AGI <chr>, At_symbol <chr>,
#   At_short_description <chr>, perc_ID <dbl>

$leaf.trtdead.DEGs.add.rL.rCR.v3.0anno
# A tibble: 3 x 11
     X1 genes  logFC logCPM    LR  PValue    FDR AGI   At_symbol
  <int> <chr>  <dbl>  <dbl> <dbl>   <dbl>  <dbl> <chr> <chr>    
1     1 BraA… -0.702  4.13   24.5 7.56e-7 0.0181 AT5G… <NA>     
2     2 BraA… -0.599  5.50   21.2 4.08e-6 0.0375 AT5G… ORP3C    
3     3 BraA… -1.92   0.414  21.0 4.71e-6 0.0375 AT5G… <NA>     
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>

$leaf.trtdead.DEGs.add.rL.rUN.v3.0anno
# A tibble: 3 x 11
     X1 genes  logFC logCPM    LR  PValue    FDR AGI   At_symbol
  <int> <chr>  <dbl>  <dbl> <dbl>   <dbl>  <dbl> <chr> <chr>    
1     1 BraA… -0.702  4.13   24.5 7.56e-7 0.0181 AT5G… <NA>     
2     2 BraA… -0.599  5.50   21.2 4.08e-6 0.0375 AT5G… ORP3C    
3     3 BraA… -1.92   0.414  21.0 4.71e-6 0.0375 AT5G… <NA>     
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>

$leaf.trtdead.DEGs.int.rL.rCR.v3.0anno
# A tibble: 370 x 11
      X1 genes  logFC logCPM    LR  PValue     FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>   <dbl>   <dbl> <chr> <chr>    
 1     1 BraA… -1.04   7.58   27.5 1.57e-7 0.00374 AT5G… AtHsp90-3
 2     2 BraA… -1.30   5.52   24.7 6.80e-7 0.00491 AT2G… <NA>     
 3     3 BraA…  1.27   4.46   23.8 1.06e-6 0.00491 AT1G… HHO6     
 4     4 BraA…  0.903  4.94   23.8 1.07e-6 0.00491 AT4G… PDE327   
 5     5 BraA…  0.964  4.89   23.6 1.19e-6 0.00491 AT5G… ATFTSZ1-1
 6     6 BraA… -1.67   3.11   23.5 1.23e-6 0.00491 AT5G… <NA>     
 7     7 BraA…  0.856  4.77   22.5 2.13e-6 0.00727 AT4G… ATCAD7   
 8     8 BraA…  2.90   0.654  21.7 3.20e-6 0.00857 AT4G… AtGGCT2;2
 9     9 BraA…  0.938  7.04   21.6 3.29e-6 0.00857 AT1G… AtPMT3   
10    10 BraA… -0.865  4.13   21.5 3.59e-6 0.00857 AT5G… <NA>     
# ... with 360 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$leaf.trtdead.DEGs.int.rL.rUN.v3.0anno
# A tibble: 0 x 11
# ... with 11 variables: X1 <int>, genes <chr>, logFC <dbl>, logCPM <dbl>,
#   LR <dbl>, PValue <dbl>, FDR <dbl>, AGI <chr>, At_symbol <chr>,
#   At_short_description <chr>, perc_ID <dbl>

$leaf.trtlive_densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno
# A tibble: 63 x 12
      X1 genes logFC.trtlive logFC.densitycr… logCPM    LR  PValue     FDR
   <int> <chr>         <dbl>            <dbl>  <dbl> <dbl>   <dbl>   <dbl>
 1     1 BraA…        0.276             0.766  7.58   29.4 4.09e-7 0.00976
 2     2 BraA…        0.489             0.376  4.13   26.8 1.54e-6 0.0177 
 3     3 BraA…       -0.758            -2.15   0.654  25.6 2.74e-6 0.0177 
 4     4 BraA…       -0.189            -0.714  4.94   25.2 3.36e-6 0.0177 
 5     5 BraA…        0.0786            1.22   5.52   24.7 4.23e-6 0.0177 
 6     6 BraA…       -0.192            -0.772  4.89   24.6 4.45e-6 0.0177 
 7     7 BraA…       -0.124            -1.14   4.46   24.1 5.93e-6 0.0186 
 8     8 BraA…       -1.25              3.95   0.659  23.9 6.59e-6 0.0186 
 9     9 BraA…       -0.0242            1.70   3.11   23.5 7.77e-6 0.0186 
10    10 BraA…       -0.916             2.00   4.58   23.5 7.80e-6 0.0186 
# ... with 53 more rows, and 4 more variables: AGI <chr>, At_symbol <chr>,
#   At_short_description <chr>, perc_ID <dbl>

$leaf.trtlive_densityun.trtlive.DEGs.int.rD.rCR.v3.0anno
# A tibble: 63 x 12
      X1 genes logFC.trtlive logFC.densityun… logCPM    LR  PValue     FDR
   <int> <chr>         <dbl>            <dbl>  <dbl> <dbl>   <dbl>   <dbl>
 1     1 BraA…         1.04            -0.766  7.58   29.4 4.09e-7 0.00976
 2     2 BraA…         0.865           -0.376  4.13   26.8 1.54e-6 0.0177 
 3     3 BraA…        -2.90             2.15   0.654  25.6 2.74e-6 0.0177 
 4     4 BraA…        -0.903            0.714  4.94   25.2 3.36e-6 0.0177 
 5     5 BraA…         1.30            -1.22   5.52   24.7 4.23e-6 0.0177 
 6     6 BraA…        -0.964            0.772  4.89   24.6 4.45e-6 0.0177 
 7     7 BraA…        -1.27             1.14   4.46   24.1 5.93e-6 0.0186 
 8     8 BraA…         2.70            -3.95   0.659  23.9 6.59e-6 0.0186 
 9     9 BraA…         1.67            -1.70   3.11   23.5 7.77e-6 0.0186 
10    10 BraA…         1.09            -2.00   4.58   23.5 7.80e-6 0.0186 
# ... with 53 more rows, and 4 more variables: AGI <chr>, At_symbol <chr>,
#   At_short_description <chr>, perc_ID <dbl>

$leaf.trtlive.DEGs.add.rD.rCR.v3.0anno
# A tibble: 3 x 11
     X1 genes logFC logCPM    LR  PValue    FDR AGI   At_symbol
  <int> <chr> <dbl>  <dbl> <dbl>   <dbl>  <dbl> <chr> <chr>    
1     1 BraA… 0.702  4.13   24.5 7.56e-7 0.0181 AT5G… <NA>     
2     2 BraA… 0.599  5.50   21.2 4.08e-6 0.0375 AT5G… ORP3C    
3     3 BraA… 1.92   0.414  21.0 4.71e-6 0.0375 AT5G… <NA>     
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>

$leaf.trtlive.DEGs.add.rD.rUN.v3.0anno
# A tibble: 3 x 11
     X1 genes logFC logCPM    LR  PValue    FDR AGI   At_symbol
  <int> <chr> <dbl>  <dbl> <dbl>   <dbl>  <dbl> <chr> <chr>    
1     1 BraA… 0.702  4.13   24.5 7.56e-7 0.0181 AT5G… <NA>     
2     2 BraA… 0.599  5.50   21.2 4.08e-6 0.0375 AT5G… ORP3C    
3     3 BraA… 1.92   0.414  21.0 4.71e-6 0.0375 AT5G… <NA>     
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>

$leaf.trtlive.DEGs.int.rD.rCR.v3.0anno
# A tibble: 370 x 11
      X1 genes  logFC logCPM    LR  PValue     FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>   <dbl>   <dbl> <chr> <chr>    
 1     1 BraA…  1.04   7.58   27.5 1.57e-7 0.00374 AT5G… AtHsp90-3
 2     2 BraA…  1.30   5.52   24.7 6.80e-7 0.00491 AT2G… <NA>     
 3     3 BraA… -1.27   4.46   23.8 1.06e-6 0.00491 AT1G… HHO6     
 4     4 BraA… -0.903  4.94   23.8 1.07e-6 0.00491 AT4G… PDE327   
 5     5 BraA… -0.964  4.89   23.6 1.19e-6 0.00491 AT5G… ATFTSZ1-1
 6     6 BraA…  1.67   3.11   23.5 1.23e-6 0.00491 AT5G… <NA>     
 7     7 BraA… -0.856  4.77   22.5 2.13e-6 0.00727 AT4G… ATCAD7   
 8     8 BraA… -2.90   0.654  21.7 3.20e-6 0.00857 AT4G… AtGGCT2;2
 9     9 BraA… -0.938  7.04   21.6 3.29e-6 0.00857 AT1G… AtPMT3   
10    10 BraA…  0.865  4.13   21.5 3.59e-6 0.00857 AT5G… <NA>     
# ... with 360 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$leaf.trtlive.DEGs.int.rD.rUN.v3.0anno
# A tibble: 0 x 11
# ... with 11 variables: X1 <int>, genes <chr>, logFC <dbl>, logCPM <dbl>,
#   LR <dbl>, PValue <dbl>, FDR <dbl>, AGI <chr>, At_symbol <chr>,
#   At_short_description <chr>, perc_ID <dbl>

$leaf.un.trtlive.DEGs.all.rD.v3.0anno
# A tibble: 0 x 11
# ... with 11 variables: X1 <int>, genes <chr>, logFC <dbl>, logCPM <dbl>,
#   LR <dbl>, PValue <dbl>, FDR <dbl>, AGI <chr>, At_symbol <chr>,
#   At_short_description <chr>, perc_ID <dbl>

$root.cr.trtlive.DEGs.all.rD.v3.0anno
# A tibble: 3,887 x 11
      X1 genes  logFC logCPM    LR   PValue      FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>    <dbl>    <dbl> <chr> <chr>    
 1     1 BraA… -1.96    4.70  87.7 7.54e-21 1.07e-16 AT1G… ASP4     
 2     2 BraA…  1.22    5.63  87.6 8.17e-21 1.07e-16 AT2G… <NA>     
 3     3 BraA…  1.28    5.28  83.6 6.07e-20 5.29e-16 AT1G… BRR2     
 4     4 BraA… -1.15    5.99  81.6 1.70e-19 1.11e-15 AT2G… <NA>     
 5     5 BraA…  1.14    7.09  75.2 4.17e-18 2.18e-14 AT1G… BRR2     
 6     6 BraA…  1.02    5.44  74.1 7.24e-18 3.16e-14 AT5G… <NA>     
 7     7 BraA…  1.94    3.77  71.4 2.91e-17 1.09e-13 AT3G… TIC      
 8     8 BraA…  0.928   7.49  69.8 6.47e-17 2.03e-13 AT2G… ATGSL03  
 9     9 BraA…  1.59    3.73  69.7 6.98e-17 2.03e-13 AT1G… ASU1     
10    10 BraA…  1.30    3.72  66.9 2.79e-16 7.10e-13 AT5G… <NA>     
# ... with 3,877 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.densitycr_densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno
# A tibble: 8,708 x 12
      X1 genes logFC.densitycr logFC.densitycr… logCPM    LR    PValue
   <int> <chr>           <dbl>            <dbl>  <dbl> <dbl>     <dbl>
 1     1 BraA…           -2.88           0.498    5.32  778. 1.17e-169
 2     2 BraA…            2.50          -0.287    4.42  511. 1.05e-111
 3     3 BraA…           -3.53           1.22     6.17  491. 2.16e-107
 4     4 BraA…           -3.95           1.12     4.01  486. 2.51e-106
 5     5 BraA…           -4.44          -0.0881   4.23  454. 2.05e- 99
 6     6 BraA…           -2.58           0.467    6.28  445. 2.56e- 97
 7     7 BraA…            2.08          -0.172    7.33  441. 2.06e- 96
 8     8 BraA…            3.07           0.696    4.36  421. 4.47e- 92
 9     9 BraA…           -3.22           0.782    5.90  383. 5.42e- 84
10    10 BraA…           -2.31           0.691    4.98  375. 3.95e- 82
# ... with 8,698 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$root.densitycr_densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno
# A tibble: 8,708 x 12
      X1 genes logFC.densitycr logFC.densitycr… logCPM    LR    PValue
   <int> <chr>           <dbl>            <dbl>  <dbl> <dbl>     <dbl>
 1     1 BraA…           -2.38          -0.498    5.32  778. 1.17e-169
 2     2 BraA…            2.21           0.287    4.42  511. 1.05e-111
 3     3 BraA…           -2.31          -1.22     6.17  491. 2.16e-107
 4     4 BraA…           -2.83          -1.12     4.01  486. 2.51e-106
 5     5 BraA…           -4.53           0.0881   4.23  454. 2.05e- 99
 6     6 BraA…           -2.11          -0.467    6.28  445. 2.56e- 97
 7     7 BraA…            1.90           0.172    7.33  441. 2.06e- 96
 8     8 BraA…            3.76          -0.696    4.36  421. 4.47e- 92
 9     9 BraA…           -2.44          -0.782    5.90  383. 5.42e- 84
10    10 BraA…           -1.62          -0.691    4.98  375. 3.95e- 82
# ... with 8,698 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$root.densitycr.DEGs.add.rD.rUN.v3.0anno
# A tibble: 8,363 x 11
      X1 genes logFC logCPM    LR    PValue       FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>     <dbl>     <dbl> <chr> <chr>    
 1     1 BraA… -2.62   5.32  656. 1.22e-144 3.21e-140 AT1G… AST56    
 2     2 BraA…  2.36   4.42  494. 1.97e-109 2.60e-105 AT1G… NLP4     
 3     3 BraA… -4.48   4.23  458. 1.38e-101 1.22e- 97 AT3G… ATIPT3   
 4     4 BraA…  1.99   7.33  436. 9.96e- 97 6.56e- 93 AT5G… AAP2     
 5     5 BraA… -2.34   6.28  395. 6.92e- 88 3.65e- 84 AT1G… ATTPPB   
 6     6 BraA…  3.38   4.35  370. 2.32e- 82 1.02e- 78 AT5G… <NA>     
 7     7 BraA…  6.68   3.06  368. 5.13e- 82 1.93e- 78 AT3G… NLP9     
 8     8 BraA… -2.47   5.28  358. 9.38e- 80 3.09e- 76 AT1G… ATATP-PR…
 9     9 BraA…  2.81   4.13  342. 1.82e- 76 5.33e- 73 AT5G… <NA>     
10    10 BraA… -3.34   4.01  336. 4.16e- 75 1.04e- 71 AT5G… <NA>     
# ... with 8,353 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.densitycr.DEGs.add.rL.rUN.v3.0anno
# A tibble: 8,363 x 11
      X1 genes logFC logCPM    LR    PValue       FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>     <dbl>     <dbl> <chr> <chr>    
 1     1 BraA… -2.62   5.32  656. 1.22e-144 3.21e-140 AT1G… AST56    
 2     2 BraA…  2.36   4.42  494. 1.97e-109 2.60e-105 AT1G… NLP4     
 3     3 BraA… -4.48   4.23  458. 1.38e-101 1.22e- 97 AT3G… ATIPT3   
 4     4 BraA…  1.99   7.33  436. 9.96e- 97 6.56e- 93 AT5G… AAP2     
 5     5 BraA… -2.34   6.28  395. 6.92e- 88 3.65e- 84 AT1G… ATTPPB   
 6     6 BraA…  3.38   4.35  370. 2.32e- 82 1.02e- 78 AT5G… <NA>     
 7     7 BraA…  6.68   3.06  368. 5.13e- 82 1.93e- 78 AT3G… NLP9     
 8     8 BraA… -2.47   5.28  358. 9.38e- 80 3.09e- 76 AT1G… ATATP-PR…
 9     9 BraA…  2.81   4.13  342. 1.82e- 76 5.33e- 73 AT5G… <NA>     
10    10 BraA… -3.34   4.01  336. 4.16e- 75 1.04e- 71 AT5G… <NA>     
# ... with 8,353 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno
# A tibble: 471 x 11
      X1 genes logFC logCPM    LR   PValue     FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>    <dbl>   <dbl> <chr> <chr>    
 1     1 BraA…  2.06  4.03   41.3 1.28e-10 3.36e-6 AT3G… BHLH039  
 2     2 BraA…  1.60  5.88   36.8 1.33e- 9 1.75e-5 AT1G… ASP4     
 3     3 BraA…  1.11  6.78   32.4 1.27e- 8 1.12e-4 AT1G… ATSBT5.2 
 4     4 BraA…  3.40  5.12   28.1 1.13e- 7 7.45e-4 AT3G… <NA>     
 5     5 BraA…  1.50  4.22   26.7 2.33e- 7 1.14e-3 AT4G… ATIRT1   
 6     6 BraA…  3.19  2.39   26.5 2.60e- 7 1.14e-3 AT1G… GAT      
 7     7 BraA…  3.72  0.831  24.9 6.10e- 7 2.10e-3 AT5G… <NA>     
 8     8 BraA…  1.72  5.26   24.8 6.39e- 7 2.10e-3 AT5G… AtCOMT   
 9     9 BraA…  2.14  5.04   24.0 9.43e- 7 2.76e-3 AT3G… F6'H1    
10    10 BraA…  1.84  4.05   23.8 1.08e- 6 2.84e-3 AT4G… <NA>     
# ... with 461 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno
# A tibble: 471 x 11
      X1 genes logFC logCPM    LR   PValue     FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>    <dbl>   <dbl> <chr> <chr>    
 1     1 BraA… -2.06  4.03   41.3 1.28e-10 3.36e-6 AT3G… BHLH039  
 2     2 BraA… -1.60  5.88   36.8 1.33e- 9 1.75e-5 AT1G… ASP4     
 3     3 BraA… -1.11  6.78   32.4 1.27e- 8 1.12e-4 AT1G… ATSBT5.2 
 4     4 BraA… -3.40  5.12   28.1 1.13e- 7 7.45e-4 AT3G… <NA>     
 5     5 BraA… -1.50  4.22   26.7 2.33e- 7 1.14e-3 AT4G… ATIRT1   
 6     6 BraA… -3.19  2.39   26.5 2.60e- 7 1.14e-3 AT1G… GAT      
 7     7 BraA… -3.72  0.831  24.9 6.10e- 7 2.10e-3 AT5G… <NA>     
 8     8 BraA… -1.72  5.26   24.8 6.39e- 7 2.10e-3 AT5G… AtCOMT   
 9     9 BraA… -2.14  5.04   24.0 9.43e- 7 2.76e-3 AT3G… F6'H1    
10    10 BraA… -1.84  4.05   23.8 1.08e- 6 2.84e-3 AT4G… <NA>     
# ... with 461 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.densityun_densityun.trtdead.DEGs.int.rL.rCR.v3.0anno
# A tibble: 8,708 x 12
      X1 genes logFC.densityun logFC.densityun… logCPM    LR    PValue
   <int> <chr>           <dbl>            <dbl>  <dbl> <dbl>     <dbl>
 1     1 BraA…            2.88          -0.498    5.32  778. 1.17e-169
 2     2 BraA…           -2.50           0.287    4.42  511. 1.05e-111
 3     3 BraA…            3.53          -1.22     6.17  491. 2.16e-107
 4     4 BraA…            3.95          -1.12     4.01  486. 2.51e-106
 5     5 BraA…            4.44           0.0881   4.23  454. 2.05e- 99
 6     6 BraA…            2.58          -0.467    6.28  445. 2.56e- 97
 7     7 BraA…           -2.08           0.172    7.33  441. 2.06e- 96
 8     8 BraA…           -3.07          -0.696    4.36  421. 4.47e- 92
 9     9 BraA…            3.22          -0.782    5.90  383. 5.42e- 84
10    10 BraA…            2.31          -0.691    4.98  375. 3.95e- 82
# ... with 8,698 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$root.densityun_densityun.trtlive.DEGs.int.rD.rCR.v3.0anno
# A tibble: 8,708 x 12
      X1 genes logFC.densityun logFC.densityun… logCPM    LR    PValue
   <int> <chr>           <dbl>            <dbl>  <dbl> <dbl>     <dbl>
 1     1 BraA…            2.38           0.498    5.32  778. 1.17e-169
 2     2 BraA…           -2.21          -0.287    4.42  511. 1.05e-111
 3     3 BraA…            2.31           1.22     6.17  491. 2.16e-107
 4     4 BraA…            2.83           1.12     4.01  486. 2.51e-106
 5     5 BraA…            4.53          -0.0881   4.23  454. 2.05e- 99
 6     6 BraA…            2.11           0.467    6.28  445. 2.56e- 97
 7     7 BraA…           -1.90          -0.172    7.33  441. 2.06e- 96
 8     8 BraA…           -3.76           0.696    4.36  421. 4.47e- 92
 9     9 BraA…            2.44           0.782    5.90  383. 5.42e- 84
10    10 BraA…            1.62           0.691    4.98  375. 3.95e- 82
# ... with 8,698 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$root.densityun.DEGs.add.rD.rCR.v3.0anno
# A tibble: 8,363 x 11
      X1 genes logFC logCPM    LR    PValue       FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>     <dbl>     <dbl> <chr> <chr>    
 1     1 BraA…  2.62   5.32  656. 1.22e-144 3.21e-140 AT1G… AST56    
 2     2 BraA… -2.36   4.42  494. 1.97e-109 2.60e-105 AT1G… NLP4     
 3     3 BraA…  4.48   4.23  458. 1.38e-101 1.22e- 97 AT3G… ATIPT3   
 4     4 BraA… -1.99   7.33  436. 9.96e- 97 6.56e- 93 AT5G… AAP2     
 5     5 BraA…  2.34   6.28  395. 6.92e- 88 3.65e- 84 AT1G… ATTPPB   
 6     6 BraA… -3.38   4.35  370. 2.32e- 82 1.02e- 78 AT5G… <NA>     
 7     7 BraA… -6.68   3.06  368. 5.13e- 82 1.93e- 78 AT3G… NLP9     
 8     8 BraA…  2.47   5.28  358. 9.38e- 80 3.09e- 76 AT1G… ATATP-PR…
 9     9 BraA… -2.81   4.13  342. 1.82e- 76 5.33e- 73 AT5G… <NA>     
10    10 BraA…  3.34   4.01  336. 4.16e- 75 1.04e- 71 AT5G… <NA>     
# ... with 8,353 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.densityun.DEGs.add.rL.rCR.v3.0anno
# A tibble: 8,363 x 11
      X1 genes logFC logCPM    LR    PValue       FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>     <dbl>     <dbl> <chr> <chr>    
 1     1 BraA…  2.62   5.32  656. 1.22e-144 3.21e-140 AT1G… AST56    
 2     2 BraA… -2.36   4.42  494. 1.97e-109 2.60e-105 AT1G… NLP4     
 3     3 BraA…  4.48   4.23  458. 1.38e-101 1.22e- 97 AT3G… ATIPT3   
 4     4 BraA… -1.99   7.33  436. 9.96e- 97 6.56e- 93 AT5G… AAP2     
 5     5 BraA…  2.34   6.28  395. 6.92e- 88 3.65e- 84 AT1G… ATTPPB   
 6     6 BraA… -3.38   4.35  370. 2.32e- 82 1.02e- 78 AT5G… <NA>     
 7     7 BraA… -6.68   3.06  368. 5.13e- 82 1.93e- 78 AT3G… NLP9     
 8     8 BraA…  2.47   5.28  358. 9.38e- 80 3.09e- 76 AT1G… ATATP-PR…
 9     9 BraA… -2.81   4.13  342. 1.82e- 76 5.33e- 73 AT5G… <NA>     
10    10 BraA…  3.34   4.01  336. 4.16e- 75 1.04e- 71 AT5G… <NA>     
# ... with 8,353 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.densityun.trtdead.DEGs.int.rL.rCR.v3.0anno
# A tibble: 471 x 12
      X1 genes logFC logCPM    LR   PValue     FDR  X1_1 AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>    <dbl>   <dbl> <int> <chr> <chr>    
 1     1 BraA… -2.06  4.03   41.3 1.28e-10 3.36e-6 15390 AT3G… BHLH039  
 2     2 BraA… -1.60  5.88   36.8 1.33e- 9 1.75e-5 35547 AT1G… ASP4     
 3     3 BraA… -1.11  6.78   32.4 1.27e- 8 1.12e-4 23863 AT1G… ATSBT5.2 
 4     4 BraA… -3.40  5.12   28.1 1.13e- 7 7.45e-4  4032 AT3G… <NA>     
 5     5 BraA… -1.50  4.22   26.7 2.33e- 7 1.14e-3  1149 AT4G… ATIRT1   
 6     6 BraA… -3.19  2.39   26.5 2.60e- 7 1.14e-3 39482 AT1G… GAT      
 7     7 BraA… -3.72  0.831  24.9 6.10e- 7 2.10e-3 28198 AT5G… <NA>     
 8     8 BraA… -1.72  5.26   24.8 6.39e- 7 2.10e-3 14171 AT5G… AtCOMT   
 9     9 BraA… -2.14  5.04   24.0 9.43e- 7 2.76e-3 21279 AT3G… F6'H1    
10    10 BraA… -1.84  4.05   23.8 1.08e- 6 2.84e-3   771 AT4G… <NA>     
# ... with 461 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.densityun.trtlive.DEGs.int.rD.rCR.v3.0anno
# A tibble: 471 x 11
      X1 genes logFC logCPM    LR   PValue     FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>    <dbl>   <dbl> <chr> <chr>    
 1     1 BraA…  2.06  4.03   41.3 1.28e-10 3.36e-6 AT3G… BHLH039  
 2     2 BraA…  1.60  5.88   36.8 1.33e- 9 1.75e-5 AT1G… ASP4     
 3     3 BraA…  1.11  6.78   32.4 1.27e- 8 1.12e-4 AT1G… ATSBT5.2 
 4     4 BraA…  3.40  5.12   28.1 1.13e- 7 7.45e-4 AT3G… <NA>     
 5     5 BraA…  1.50  4.22   26.7 2.33e- 7 1.14e-3 AT4G… ATIRT1   
 6     6 BraA…  3.19  2.39   26.5 2.60e- 7 1.14e-3 AT1G… GAT      
 7     7 BraA…  3.72  0.831  24.9 6.10e- 7 2.10e-3 AT5G… <NA>     
 8     8 BraA…  1.72  5.26   24.8 6.39e- 7 2.10e-3 AT5G… AtCOMT   
 9     9 BraA…  2.14  5.04   24.0 9.43e- 7 2.76e-3 AT3G… F6'H1    
10    10 BraA…  1.84  4.05   23.8 1.08e- 6 2.84e-3 AT4G… <NA>     
# ... with 461 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.trtdead_densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno
# A tibble: 3,857 x 12
      X1 genes logFC.trtdead logFC.densitycr… logCPM    LR   PValue
   <int> <chr>         <dbl>            <dbl>  <dbl> <dbl>    <dbl>
 1     1 BraA…        0.370             1.60    5.88 105.  1.40e-23
 2     2 BraA…        0.0552            2.06    4.03  77.8 1.27e-17
 3     3 BraA…        0.372             0.682   6.91  73.4 1.16e-16
 4     4 BraA…        0.211             1.50    4.22  65.5 5.99e-15
 5     5 BraA…       -0.523            -0.132   8.54  63.6 1.56e-14
 6     6 BraA…       -0.331            -0.590   7.24  60.6 6.97e-14
 7     7 BraA…       -2.20              1.84    2.44  59.1 1.50e-13
 8     8 BraA…       -2.52              1.41    1.76  58.1 2.36e-13
 9     9 BraA…       -0.128            -0.895   5.25  56.8 4.62e-13
10    10 BraA…       -0.231            -0.989   5.48  55.3 9.90e-13
# ... with 3,847 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$root.trtdead_densityun.trtdead.DEGs.int.rL.rCR.v3.0anno
# A tibble: 3,857 x 12
      X1 genes logFC.trtdead logFC.densityun… logCPM    LR   PValue
   <int> <chr>         <dbl>            <dbl>  <dbl> <dbl>    <dbl>
 1     1 BraA…         1.97            -1.60    5.88 105.  1.40e-23
 2     2 BraA…         2.11            -2.06    4.03  77.8 1.27e-17
 3     3 BraA…         1.05            -0.682   6.91  73.4 1.16e-16
 4     4 BraA…         1.71            -1.50    4.22  65.5 5.99e-15
 5     5 BraA…        -0.655            0.132   8.54  63.6 1.56e-14
 6     6 BraA…        -0.921            0.590   7.24  60.6 6.97e-14
 7     7 BraA…        -0.353           -1.84    2.44  59.1 1.50e-13
 8     8 BraA…        -1.12            -1.41    1.76  58.1 2.36e-13
 9     9 BraA…        -1.02             0.895   5.25  56.8 4.62e-13
10    10 BraA…        -1.22             0.989   5.48  55.3 9.90e-13
# ... with 3,847 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$root.trtdead.DEGs.add.rL.rCR.v3.0anno
# A tibble: 3,352 x 11
      X1 genes  logFC logCPM    LR   PValue      FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>    <dbl>    <dbl> <chr> <chr>    
 1     1 BraA… -0.590   8.54  62.3 2.94e-15 7.74e-11 AT2G… ATUBC24  
 2     2 BraA…  2.18    1.59  55.7 8.55e-14 1.13e- 9 AT2G… <NA>     
 3     3 BraA…  1.10    2.65  49.2 2.27e-12 1.99e- 8 AT1G… <NA>     
 4     4 BraA…  0.482   6.84  46.0 1.17e-11 7.35e- 8 AT4G… <NA>     
 5     5 BraA… -1.61    1.61  45.3 1.67e-11 7.35e- 8 AT1G… IGMT2    
 6     6 BraA…  0.607   5.95  45.3 1.68e-11 7.35e- 8 AT2G… ATGSTU4  
 7     7 BraA… -0.528   6.88  44.9 2.07e-11 7.35e- 8 AT1G… ABCG35   
 8     8 BraA… -0.499   7.51  44.8 2.23e-11 7.35e- 8 AT1G… FB       
 9     9 BraA…  0.714   6.91  44.0 3.36e-11 9.82e- 8 AT1G… ATOPR2   
10    10 BraA… -0.569   6.15  43.5 4.27e-11 1.13e- 7 AT5G… CLPD     
# ... with 3,342 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.trtdead.DEGs.add.rL.rUN.v3.0anno
# A tibble: 3,352 x 11
      X1 genes  logFC logCPM    LR   PValue      FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>    <dbl>    <dbl> <chr> <chr>    
 1     1 BraA… -0.590   8.54  62.3 2.94e-15 7.74e-11 AT2G… ATUBC24  
 2     2 BraA…  2.18    1.59  55.7 8.55e-14 1.13e- 9 AT2G… <NA>     
 3     3 BraA…  1.10    2.65  49.2 2.27e-12 1.99e- 8 AT1G… <NA>     
 4     4 BraA…  0.482   6.84  46.0 1.17e-11 7.35e- 8 AT4G… <NA>     
 5     5 BraA… -1.61    1.61  45.3 1.67e-11 7.35e- 8 AT1G… IGMT2    
 6     6 BraA…  0.607   5.95  45.3 1.68e-11 7.35e- 8 AT2G… ATGSTU4  
 7     7 BraA… -0.528   6.88  44.9 2.07e-11 7.35e- 8 AT1G… ABCG35   
 8     8 BraA… -0.499   7.51  44.8 2.23e-11 7.35e- 8 AT1G… FB       
 9     9 BraA…  0.714   6.91  44.0 3.36e-11 9.82e- 8 AT1G… ATOPR2   
10    10 BraA… -0.569   6.15  43.5 4.27e-11 1.13e- 7 AT5G… CLPD     
# ... with 3,342 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.trtdead.DEGs.int.rL.rCR.v3.0anno
# A tibble: 3,434 x 11
      X1 genes  logFC logCPM    LR   PValue      FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>    <dbl>    <dbl> <chr> <chr>    
 1     1 BraA…  1.97    5.88 101.  9.26e-24 2.44e-19 AT1G… ASP4     
 2     2 BraA…  2.11    4.03  77.7 1.18e-18 1.55e-14 AT3G… BHLH039  
 3     3 BraA…  1.05    6.91  65.1 7.00e-16 6.15e-12 AT1G… ATOPR2   
 4     4 BraA…  1.71    4.22  64.3 1.05e-15 6.92e-12 AT4G… ATIRT1   
 5     5 BraA… -1.02    5.25  55.9 7.52e-14 3.96e-10 AT5G… <NA>     
 6     6 BraA… -0.921   7.24  53.6 2.47e-13 1.07e- 9 AT2G… ATGSL03  
 7     7 BraA… -1.22    5.48  53.3 2.83e-13 1.07e- 9 AT2G… <NA>     
 8     8 BraA…  1.81    5.26  51.7 6.49e-13 2.14e- 9 AT5G… AtCOMT   
 9     9 BraA…  1.16    5.96  50.9 9.52e-13 2.30e- 9 AT2G… <NA>     
10    10 BraA… -1.24    3.91  50.9 9.83e-13 2.30e- 9 AT4G… ATSPS4F  
# ... with 3,424 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.trtdead.DEGs.int.rL.rUN.v3.0anno
# A tibble: 357 x 11
      X1 genes  logFC logCPM    LR   PValue      FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>    <dbl>    <dbl> <chr> <chr>    
 1     1 BraA… -2.20   2.44   57.3 3.75e-14 9.87e-10 AT1G… ATGSTU12 
 2     2 BraA… -2.52   1.76   47.1 6.73e-12 7.82e- 8 AT2G… ATWRKY59 
 3     3 BraA… -4.03   0.831  46.6 8.91e-12 7.82e- 8 AT5G… <NA>     
 4     4 BraA… -1.40   3.53   41.0 1.52e-10 1.00e- 6 AT1G… HMS      
 5     5 BraA… -1.35   2.35   38.1 6.87e-10 3.27e- 6 AT2G… ANAC042  
 6     6 BraA… -2.08   3.27   37.9 7.45e-10 3.27e- 6 AT2G… <NA>     
 7     7 BraA… -1.97   5.83   34.1 5.13e- 9 1.93e- 5 AT4G… <NA>     
 8     8 BraA… -0.925  4.26   32.6 1.15e- 8 3.70e- 5 AT4G… CYP706A1 
 9     9 BraA… -1.86   2.87   32.4 1.26e- 8 3.70e- 5 AT2G… ANAC042  
10    10 BraA… -1.90   1.61   31.8 1.70e- 8 4.47e- 5 AT1G… IGMT2    
# ... with 347 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.trtlive_densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno
# A tibble: 3,857 x 12
      X1 genes logFC.trtlive logFC.densitycr… logCPM    LR   PValue
   <int> <chr>         <dbl>            <dbl>  <dbl> <dbl>    <dbl>
 1     1 BraA…       -0.370            -1.60    5.88 105.  1.40e-23
 2     2 BraA…       -0.0552           -2.06    4.03  77.8 1.27e-17
 3     3 BraA…       -0.372            -0.682   6.91  73.4 1.16e-16
 4     4 BraA…       -0.211            -1.50    4.22  65.5 5.99e-15
 5     5 BraA…        0.523             0.132   8.54  63.6 1.56e-14
 6     6 BraA…        0.331             0.590   7.24  60.6 6.97e-14
 7     7 BraA…        2.20             -1.84    2.44  59.1 1.50e-13
 8     8 BraA…        2.52             -1.41    1.76  58.1 2.36e-13
 9     9 BraA…        0.128             0.895   5.25  56.8 4.62e-13
10    10 BraA…        0.231             0.989   5.48  55.3 9.90e-13
# ... with 3,847 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$root.trtlive_densityun.trtlive.DEGs.int.rD.rCR.v3.0anno
# A tibble: 3,857 x 12
      X1 genes logFC.trtlive logFC.densityun… logCPM    LR   PValue
   <int> <chr>         <dbl>            <dbl>  <dbl> <dbl>    <dbl>
 1     1 BraA…        -1.97             1.60    5.88 105.  1.40e-23
 2     2 BraA…        -2.11             2.06    4.03  77.8 1.27e-17
 3     3 BraA…        -1.05             0.682   6.91  73.4 1.16e-16
 4     4 BraA…        -1.71             1.50    4.22  65.5 5.99e-15
 5     5 BraA…         0.655           -0.132   8.54  63.6 1.56e-14
 6     6 BraA…         0.921           -0.590   7.24  60.6 6.97e-14
 7     7 BraA…         0.353            1.84    2.44  59.1 1.50e-13
 8     8 BraA…         1.12             1.41    1.76  58.1 2.36e-13
 9     9 BraA…         1.02            -0.895   5.25  56.8 4.62e-13
10    10 BraA…         1.22            -0.989   5.48  55.3 9.90e-13
# ... with 3,847 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$root.trtlive.DEGs.add.rD.rCR.v3.0anno
# A tibble: 3,352 x 11
      X1 genes  logFC logCPM    LR   PValue      FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>    <dbl>    <dbl> <chr> <chr>    
 1     1 BraA…  0.590   8.54  62.3 2.94e-15 7.74e-11 AT2G… ATUBC24  
 2     2 BraA… -2.18    1.59  55.7 8.55e-14 1.13e- 9 AT2G… <NA>     
 3     3 BraA… -1.10    2.65  49.2 2.27e-12 1.99e- 8 AT1G… <NA>     
 4     4 BraA… -0.482   6.84  46.0 1.17e-11 7.35e- 8 AT4G… <NA>     
 5     5 BraA…  1.61    1.61  45.3 1.67e-11 7.35e- 8 AT1G… IGMT2    
 6     6 BraA… -0.607   5.95  45.3 1.68e-11 7.35e- 8 AT2G… ATGSTU4  
 7     7 BraA…  0.528   6.88  44.9 2.07e-11 7.35e- 8 AT1G… ABCG35   
 8     8 BraA…  0.499   7.51  44.8 2.23e-11 7.35e- 8 AT1G… FB       
 9     9 BraA… -0.714   6.91  44.0 3.36e-11 9.82e- 8 AT1G… ATOPR2   
10    10 BraA…  0.569   6.15  43.5 4.27e-11 1.13e- 7 AT5G… CLPD     
# ... with 3,342 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.trtlive.DEGs.add.rD.rUN.v3.0anno
# A tibble: 3,352 x 11
      X1 genes  logFC logCPM    LR   PValue      FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>    <dbl>    <dbl> <chr> <chr>    
 1     1 BraA…  0.590   8.54  62.3 2.94e-15 7.74e-11 AT2G… ATUBC24  
 2     2 BraA… -2.18    1.59  55.7 8.55e-14 1.13e- 9 AT2G… <NA>     
 3     3 BraA… -1.10    2.65  49.2 2.27e-12 1.99e- 8 AT1G… <NA>     
 4     4 BraA… -0.482   6.84  46.0 1.17e-11 7.35e- 8 AT4G… <NA>     
 5     5 BraA…  1.61    1.61  45.3 1.67e-11 7.35e- 8 AT1G… IGMT2    
 6     6 BraA… -0.607   5.95  45.3 1.68e-11 7.35e- 8 AT2G… ATGSTU4  
 7     7 BraA…  0.528   6.88  44.9 2.07e-11 7.35e- 8 AT1G… ABCG35   
 8     8 BraA…  0.499   7.51  44.8 2.23e-11 7.35e- 8 AT1G… FB       
 9     9 BraA… -0.714   6.91  44.0 3.36e-11 9.82e- 8 AT1G… ATOPR2   
10    10 BraA…  0.569   6.15  43.5 4.27e-11 1.13e- 7 AT5G… CLPD     
# ... with 3,342 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.trtlive.DEGs.int.rD.rCR.v3.0anno
# A tibble: 3,434 x 11
      X1 genes  logFC logCPM    LR   PValue      FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>    <dbl>    <dbl> <chr> <chr>    
 1     1 BraA… -1.97    5.88 101.  9.26e-24 2.44e-19 AT1G… ASP4     
 2     2 BraA… -2.11    4.03  77.7 1.18e-18 1.55e-14 AT3G… BHLH039  
 3     3 BraA… -1.05    6.91  65.1 7.00e-16 6.15e-12 AT1G… ATOPR2   
 4     4 BraA… -1.71    4.22  64.3 1.05e-15 6.92e-12 AT4G… ATIRT1   
 5     5 BraA…  1.02    5.25  55.9 7.52e-14 3.96e-10 AT5G… <NA>     
 6     6 BraA…  0.921   7.24  53.6 2.47e-13 1.07e- 9 AT2G… ATGSL03  
 7     7 BraA…  1.22    5.48  53.3 2.83e-13 1.07e- 9 AT2G… <NA>     
 8     8 BraA… -1.81    5.26  51.7 6.49e-13 2.14e- 9 AT5G… AtCOMT   
 9     9 BraA… -1.16    5.96  50.9 9.52e-13 2.30e- 9 AT2G… <NA>     
10    10 BraA…  1.24    3.91  50.9 9.83e-13 2.30e- 9 AT4G… ATSPS4F  
# ... with 3,424 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.trtlive.DEGs.int.rD.rUN.v3.0anno
# A tibble: 357 x 11
      X1 genes logFC logCPM    LR   PValue      FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>    <dbl>    <dbl> <chr> <chr>    
 1     1 BraA… 2.20   2.44   57.3 3.75e-14 9.87e-10 AT1G… ATGSTU12 
 2     2 BraA… 2.52   1.76   47.1 6.73e-12 7.82e- 8 AT2G… ATWRKY59 
 3     3 BraA… 4.03   0.831  46.6 8.91e-12 7.82e- 8 AT5G… <NA>     
 4     4 BraA… 1.40   3.53   41.0 1.52e-10 1.00e- 6 AT1G… HMS      
 5     5 BraA… 1.35   2.35   38.1 6.87e-10 3.27e- 6 AT2G… ANAC042  
 6     6 BraA… 2.08   3.27   37.9 7.45e-10 3.27e- 6 AT2G… <NA>     
 7     7 BraA… 1.97   5.83   34.1 5.13e- 9 1.93e- 5 AT4G… <NA>     
 8     8 BraA… 0.925  4.26   32.6 1.15e- 8 3.70e- 5 AT4G… CYP706A1 
 9     9 BraA… 1.86   2.87   32.4 1.26e- 8 3.70e- 5 AT2G… ANAC042  
10    10 BraA… 1.90   1.61   31.8 1.70e- 8 4.47e- 5 AT1G… IGMT2    
# ... with 347 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.un.trtlive.DEGs.all.rD.v3.0anno
# A tibble: 297 x 11
      X1 genes  logFC logCPM    LR   PValue     FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>    <dbl>   <dbl> <chr> <chr>    
 1     1 BraA…  2.19   2.37   56.7 5.00e-14 1.30e-9 AT1G… ATGSTU12 
 2     2 BraA…  2.06   3.30   47.4 5.87e-12 5.83e-8 AT2G… <NA>     
 3     3 BraA…  4.05   0.567  47.1 6.75e-12 5.83e-8 AT5G… <NA>     
 4     4 BraA…  2.52   1.68   46.1 1.13e-11 7.29e-8 AT2G… ATWRKY59 
 5     5 BraA… -2.17   1.80   45.7 1.41e-11 7.32e-8 AT2G… <NA>     
 6     6 BraA…  1.41   2.87   43.4 4.55e-11 1.97e-7 AT1G… HMS      
 7     7 BraA…  1.86   2.20   38.3 5.95e-10 2.20e-6 AT2G… ANAC042  
 8     8 BraA…  0.933  4.20   38.0 7.03e-10 2.28e-6 AT4G… CYP706A1 
 9     9 BraA…  1.46   1.59   37.5 9.38e-10 2.70e-6 AT5G… <NA>     
10    10 BraA…  1.90   1.67   36.6 1.48e- 9 3.84e-6 AT1G… IGMT2    
# ... with 287 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>
map(DEG.count.list.e3.v3.0annotation.all,~filter(.x,FDR<0.05)) # does work
$leaf.cr.trtlive.DEGs.all.rD.v3.0anno
# A tibble: 12 x 11
      X1 genes  logFC logCPM    LR  PValue    FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>   <dbl>  <dbl> <chr> <chr>    
 1     1 BraA…  2.75   2.86   20.6 5.77e-6 0.0413 AT1G… <NA>     
 2     2 BraA…  1.05   8.17   19.2 1.19e-5 0.0413 AT5G… AtHsp90-3
 3     3 BraA… -3.07   0.296  18.7 1.49e-5 0.0413 AT2G… PLAT2    
 4     4 BraA…  2.69   0.508  18.7 1.50e-5 0.0413 AT1G… <NA>     
 5     5 BraA… -0.961  7.30   18.7 1.51e-5 0.0413 AT1G… AtPMT3   
 6     6 BraA…  1.64   3.71   18.7 1.51e-5 0.0413 AT5G… AAP4     
 7     7 BraA…  1.66   2.15   18.7 1.54e-5 0.0413 AT2G… ArathEUL…
 8     8 BraA… -0.846  4.97   18.5 1.71e-5 0.0413 AT4G… ATCAD7   
 9     9 BraA…  1.68   3.95   18.3 1.89e-5 0.0413 AT5G… <NA>     
10    10 BraA…  2.83   1.000  18.3 1.91e-5 0.0413 AT5G… ANAC092  
11    11 BraA…  2.35   2.04   18.2 1.94e-5 0.0413 AT5G… <NA>     
12    12 BraA…  1.67   2.20   17.8 2.40e-5 0.0469 AT5G… <NA>     
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>

$leaf.densitycr_densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno
# A tibble: 14,074 x 12
      X1 genes logFC.densitycr logFC.densitycr… logCPM    LR    PValue
   <int> <chr>           <dbl>            <dbl>  <dbl> <dbl>     <dbl>
 1     1 BraA…           -7.74          1.09      4.09  891. 2.88e-194
 2     2 BraA…           -2.65          0.0205    8.15  664. 7.63e-145
 3     3 BraA…           -2.66         -0.00762   7.37  574. 1.78e-125
 4     4 BraA…            3.98          0.267     7.24  510. 1.56e-111
 5     5 BraA…           -4.47          0.399     7.29  494. 6.31e-108
 6     6 BraA…           -2.65          0.139     7.53  491. 1.88e-107
 7     7 BraA…           -2.11         -0.281     6.87  477. 2.91e-104
 8     8 BraA…           -3.09          0.124     5.97  471. 5.85e-103
 9     9 BraA…           -3.07         -0.179     7.57  470. 7.61e-103
10    10 BraA…           -2.45         -0.0962    4.91  467. 3.40e-102
# ... with 14,064 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$leaf.densitycr_densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno
# A tibble: 14,074 x 12
      X1 genes logFC.densitycr logFC.densitycr… logCPM    LR    PValue
   <int> <chr>           <dbl>            <dbl>  <dbl> <dbl>     <dbl>
 1     1 BraA…           -6.65         -1.09      4.09  891. 2.88e-194
 2     2 BraA…           -2.63         -0.0205    8.15  664. 7.63e-145
 3     3 BraA…           -2.67          0.00762   7.37  574. 1.78e-125
 4     4 BraA…            4.25         -0.267     7.24  510. 1.56e-111
 5     5 BraA…           -4.07         -0.399     7.29  494. 6.31e-108
 6     6 BraA…           -2.51         -0.139     7.53  491. 1.88e-107
 7     7 BraA…           -2.39          0.281     6.87  477. 2.91e-104
 8     8 BraA…           -2.97         -0.124     5.97  471. 5.85e-103
 9     9 BraA…           -3.25          0.179     7.57  470. 7.61e-103
10    10 BraA…           -2.55          0.0962    4.91  467. 3.40e-102
# ... with 14,064 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$leaf.densitycr.DEGs.add.rD.rUN.v3.0anno
# A tibble: 14,919 x 11
      X1 genes logFC logCPM    LR    PValue       FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>     <dbl>     <dbl> <chr> <chr>    
 1     1 BraA… -7.03   4.09  860. 5.16e-189 1.23e-184 AT1G… ARR4     
 2     2 BraA… -2.64   8.15  678. 1.81e-149 2.16e-145 AT5G… RPL4     
 3     3 BraA… -2.67   7.37  588. 6.29e-130 5.01e-126 AT1G… ARP1     
 4     4 BraA…  4.11   7.24  512. 2.09e-113 1.25e-109 AT5G… <NA>     
 5     5 BraA… -2.58   7.53  497. 3.90e-110 1.86e-106 AT4G… HLN      
 6     6 BraA… -4.26   7.29  485. 1.51e-107 6.00e-104 AT5G… ATHD2    
 7     7 BraA… -3.03   5.97  480. 1.91e-106 6.52e-103 AT3G… <NA>     
 8     8 BraA… -2.50   4.91  478. 6.82e-106 2.04e-102 AT2G… ASHR2    
 9     9 BraA… -3.16   7.57  475. 2.11e-105 5.60e-102 AT5G… ATHD2    
10    10 BraA… -2.25   6.87  460. 5.80e-102 1.39e- 98 AT5G… NAP1;3   
# ... with 14,909 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$leaf.densitycr.DEGs.add.rL.rUN.v3.0anno
# A tibble: 14,919 x 11
      X1 genes logFC logCPM    LR    PValue       FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>     <dbl>     <dbl> <chr> <chr>    
 1     1 BraA… -7.03   4.09  860. 5.16e-189 1.23e-184 AT1G… ARR4     
 2     2 BraA… -2.64   8.15  678. 1.81e-149 2.16e-145 AT5G… RPL4     
 3     3 BraA… -2.67   7.37  588. 6.29e-130 5.01e-126 AT1G… ARP1     
 4     4 BraA…  4.11   7.24  512. 2.09e-113 1.25e-109 AT5G… <NA>     
 5     5 BraA… -2.58   7.53  497. 3.90e-110 1.86e-106 AT4G… HLN      
 6     6 BraA… -4.26   7.29  485. 1.51e-107 6.00e-104 AT5G… ATHD2    
 7     7 BraA… -3.03   5.97  480. 1.91e-106 6.52e-103 AT3G… <NA>     
 8     8 BraA… -2.50   4.91  478. 6.82e-106 2.04e-102 AT2G… ASHR2    
 9     9 BraA… -3.16   7.57  475. 2.11e-105 5.60e-102 AT5G… ATHD2    
10    10 BraA… -2.25   6.87  460. 5.80e-102 1.39e- 98 AT5G… NAP1;3   
# ... with 14,909 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$leaf.densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno
# A tibble: 2 x 11
     X1 genes logFC logCPM    LR  PValue    FDR AGI   At_symbol
  <int> <chr> <dbl>  <dbl> <dbl>   <dbl>  <dbl> <chr> <chr>    
1     1 BraA… -2.00  4.58   22.9 1.69e-6 0.0271 AT1G… ARR7     
2     2 BraA… -3.95  0.659  22.3 2.27e-6 0.0271 AT1G… <NA>     
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>

$leaf.densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno
# A tibble: 2 x 11
     X1 genes logFC logCPM    LR  PValue    FDR AGI   At_symbol
  <int> <chr> <dbl>  <dbl> <dbl>   <dbl>  <dbl> <chr> <chr>    
1     1 BraA…  2.00  4.58   22.9 1.69e-6 0.0271 AT1G… ARR7     
2     2 BraA…  3.95  0.659  22.3 2.27e-6 0.0271 AT1G… <NA>     
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>

$leaf.densityun_densityun.trtdead.DEGs.int.rL.rCR.v3.0anno
# A tibble: 14,074 x 12
      X1 genes logFC.densityun logFC.densityun… logCPM    LR    PValue
   <int> <chr>           <dbl>            <dbl>  <dbl> <dbl>     <dbl>
 1     1 BraA…            7.74         -1.09      4.09  891. 2.88e-194
 2     2 BraA…            2.65         -0.0205    8.15  664. 7.63e-145
 3     3 BraA…            2.66          0.00762   7.37  574. 1.78e-125
 4     4 BraA…           -3.98         -0.267     7.24  510. 1.56e-111
 5     5 BraA…            4.47         -0.399     7.29  494. 6.31e-108
 6     6 BraA…            2.65         -0.139     7.53  491. 1.88e-107
 7     7 BraA…            2.11          0.281     6.87  477. 2.91e-104
 8     8 BraA…            3.09         -0.124     5.97  471. 5.85e-103
 9     9 BraA…            3.07          0.179     7.57  470. 7.61e-103
10    10 BraA…            2.45          0.0962    4.91  467. 3.40e-102
# ... with 14,064 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$leaf.densityun_densityun.trtlive.DEGs.int.rD.rCR.v3.0anno
# A tibble: 14,074 x 12
      X1 genes logFC.densityun logFC.densityun… logCPM    LR    PValue
   <int> <chr>           <dbl>            <dbl>  <dbl> <dbl>     <dbl>
 1     1 BraA…            6.65          1.09      4.09  891. 2.88e-194
 2     2 BraA…            2.63          0.0205    8.15  664. 7.63e-145
 3     3 BraA…            2.67         -0.00762   7.37  574. 1.78e-125
 4     4 BraA…           -4.25          0.267     7.24  510. 1.56e-111
 5     5 BraA…            4.07          0.399     7.29  494. 6.31e-108
 6     6 BraA…            2.51          0.139     7.53  491. 1.88e-107
 7     7 BraA…            2.39         -0.281     6.87  477. 2.91e-104
 8     8 BraA…            2.97          0.124     5.97  471. 5.85e-103
 9     9 BraA…            3.25         -0.179     7.57  470. 7.61e-103
10    10 BraA…            2.55         -0.0962    4.91  467. 3.40e-102
# ... with 14,064 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$leaf.densityun.DEGs.add.rD.rCR.v3.0anno
# A tibble: 14,919 x 11
      X1 genes logFC logCPM    LR    PValue       FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>     <dbl>     <dbl> <chr> <chr>    
 1     1 BraA…  7.03   4.09  860. 5.16e-189 1.23e-184 AT1G… ARR4     
 2     2 BraA…  2.64   8.15  678. 1.81e-149 2.16e-145 AT5G… RPL4     
 3     3 BraA…  2.67   7.37  588. 6.29e-130 5.01e-126 AT1G… ARP1     
 4     4 BraA… -4.11   7.24  512. 2.09e-113 1.25e-109 AT5G… <NA>     
 5     5 BraA…  2.58   7.53  497. 3.90e-110 1.86e-106 AT4G… HLN      
 6     6 BraA…  4.26   7.29  485. 1.51e-107 6.00e-104 AT5G… ATHD2    
 7     7 BraA…  3.03   5.97  480. 1.91e-106 6.52e-103 AT3G… <NA>     
 8     8 BraA…  2.50   4.91  478. 6.82e-106 2.04e-102 AT2G… ASHR2    
 9     9 BraA…  3.16   7.57  475. 2.11e-105 5.60e-102 AT5G… ATHD2    
10    10 BraA…  2.25   6.87  460. 5.80e-102 1.39e- 98 AT5G… NAP1;3   
# ... with 14,909 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$leaf.densityun.DEGs.add.rL.rCR.v3.0anno
# A tibble: 14,919 x 11
      X1 genes logFC logCPM    LR    PValue       FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>     <dbl>     <dbl> <chr> <chr>    
 1     1 BraA…  7.03   4.09  860. 5.16e-189 1.23e-184 AT1G… ARR4     
 2     2 BraA…  2.64   8.15  678. 1.81e-149 2.16e-145 AT5G… RPL4     
 3     3 BraA…  2.67   7.37  588. 6.29e-130 5.01e-126 AT1G… ARP1     
 4     4 BraA… -4.11   7.24  512. 2.09e-113 1.25e-109 AT5G… <NA>     
 5     5 BraA…  2.58   7.53  497. 3.90e-110 1.86e-106 AT4G… HLN      
 6     6 BraA…  4.26   7.29  485. 1.51e-107 6.00e-104 AT5G… ATHD2    
 7     7 BraA…  3.03   5.97  480. 1.91e-106 6.52e-103 AT3G… <NA>     
 8     8 BraA…  2.50   4.91  478. 6.82e-106 2.04e-102 AT2G… ASHR2    
 9     9 BraA…  3.16   7.57  475. 2.11e-105 5.60e-102 AT5G… ATHD2    
10    10 BraA…  2.25   6.87  460. 5.80e-102 1.39e- 98 AT5G… NAP1;3   
# ... with 14,909 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$leaf.densityun.trtdead.DEGs.int.rL.rCR.v3.0anno
# A tibble: 2 x 12
     X1 genes logFC logCPM    LR  PValue    FDR  X1_1 AGI   At_symbol
  <int> <chr> <dbl>  <dbl> <dbl>   <dbl>  <dbl> <int> <chr> <chr>    
1     1 BraA…  2.00  4.58   22.9 1.69e-6 0.0271 23774 AT1G… ARR7     
2     2 BraA…  3.95  0.659  22.3 2.27e-6 0.0271 33024 AT1G… <NA>     
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>

$leaf.densityun.trtlive.DEGs.int.rD.rCR.v3.0anno
# A tibble: 2 x 11
     X1 genes logFC logCPM    LR  PValue    FDR AGI   At_symbol
  <int> <chr> <dbl>  <dbl> <dbl>   <dbl>  <dbl> <chr> <chr>    
1     1 BraA… -2.00  4.58   22.9 1.69e-6 0.0271 AT1G… ARR7     
2     2 BraA… -3.95  0.659  22.3 2.27e-6 0.0271 AT1G… <NA>     
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>

$leaf.trtdead_densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno
# A tibble: 63 x 12
      X1 genes logFC.trtdead logFC.densitycr… logCPM    LR  PValue     FDR
   <int> <chr>         <dbl>            <dbl>  <dbl> <dbl>   <dbl>   <dbl>
 1     1 BraA…       -0.276            -0.766  7.58   29.4 4.09e-7 0.00976
 2     2 BraA…       -0.489            -0.376  4.13   26.8 1.54e-6 0.0177 
 3     3 BraA…        0.758             2.15   0.654  25.6 2.74e-6 0.0177 
 4     4 BraA…        0.189             0.714  4.94   25.2 3.36e-6 0.0177 
 5     5 BraA…       -0.0786           -1.22   5.52   24.7 4.23e-6 0.0177 
 6     6 BraA…        0.192             0.772  4.89   24.6 4.45e-6 0.0177 
 7     7 BraA…        0.124             1.14   4.46   24.1 5.93e-6 0.0186 
 8     8 BraA…        1.25             -3.95   0.659  23.9 6.59e-6 0.0186 
 9     9 BraA…        0.0242           -1.70   3.11   23.5 7.77e-6 0.0186 
10    10 BraA…        0.916            -2.00   4.58   23.5 7.80e-6 0.0186 
# ... with 53 more rows, and 4 more variables: AGI <chr>, At_symbol <chr>,
#   At_short_description <chr>, perc_ID <dbl>

$leaf.trtdead_densityun.trtdead.DEGs.int.rL.rCR.v3.0anno
# A tibble: 63 x 12
      X1 genes logFC.trtdead logFC.densityun… logCPM    LR  PValue     FDR
   <int> <chr>         <dbl>            <dbl>  <dbl> <dbl>   <dbl>   <dbl>
 1     1 BraA…        -1.04             0.766  7.58   29.4 4.09e-7 0.00976
 2     2 BraA…        -0.865            0.376  4.13   26.8 1.54e-6 0.0177 
 3     3 BraA…         2.90            -2.15   0.654  25.6 2.74e-6 0.0177 
 4     4 BraA…         0.903           -0.714  4.94   25.2 3.36e-6 0.0177 
 5     5 BraA…        -1.30             1.22   5.52   24.7 4.23e-6 0.0177 
 6     6 BraA…         0.964           -0.772  4.89   24.6 4.45e-6 0.0177 
 7     7 BraA…         1.27            -1.14   4.46   24.1 5.93e-6 0.0186 
 8     8 BraA…        -2.70             3.95   0.659  23.9 6.59e-6 0.0186 
 9     9 BraA…        -1.67             1.70   3.11   23.5 7.77e-6 0.0186 
10    10 BraA…        -1.09             2.00   4.58   23.5 7.80e-6 0.0186 
# ... with 53 more rows, and 4 more variables: AGI <chr>, At_symbol <chr>,
#   At_short_description <chr>, perc_ID <dbl>

$leaf.trtdead.DEGs.add.rL.rCR.v3.0anno
# A tibble: 3 x 11
     X1 genes  logFC logCPM    LR  PValue    FDR AGI   At_symbol
  <int> <chr>  <dbl>  <dbl> <dbl>   <dbl>  <dbl> <chr> <chr>    
1     1 BraA… -0.702  4.13   24.5 7.56e-7 0.0181 AT5G… <NA>     
2     2 BraA… -0.599  5.50   21.2 4.08e-6 0.0375 AT5G… ORP3C    
3     3 BraA… -1.92   0.414  21.0 4.71e-6 0.0375 AT5G… <NA>     
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>

$leaf.trtdead.DEGs.add.rL.rUN.v3.0anno
# A tibble: 3 x 11
     X1 genes  logFC logCPM    LR  PValue    FDR AGI   At_symbol
  <int> <chr>  <dbl>  <dbl> <dbl>   <dbl>  <dbl> <chr> <chr>    
1     1 BraA… -0.702  4.13   24.5 7.56e-7 0.0181 AT5G… <NA>     
2     2 BraA… -0.599  5.50   21.2 4.08e-6 0.0375 AT5G… ORP3C    
3     3 BraA… -1.92   0.414  21.0 4.71e-6 0.0375 AT5G… <NA>     
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>

$leaf.trtdead.DEGs.int.rL.rCR.v3.0anno
# A tibble: 370 x 11
      X1 genes  logFC logCPM    LR  PValue     FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>   <dbl>   <dbl> <chr> <chr>    
 1     1 BraA… -1.04   7.58   27.5 1.57e-7 0.00374 AT5G… AtHsp90-3
 2     2 BraA… -1.30   5.52   24.7 6.80e-7 0.00491 AT2G… <NA>     
 3     3 BraA…  1.27   4.46   23.8 1.06e-6 0.00491 AT1G… HHO6     
 4     4 BraA…  0.903  4.94   23.8 1.07e-6 0.00491 AT4G… PDE327   
 5     5 BraA…  0.964  4.89   23.6 1.19e-6 0.00491 AT5G… ATFTSZ1-1
 6     6 BraA… -1.67   3.11   23.5 1.23e-6 0.00491 AT5G… <NA>     
 7     7 BraA…  0.856  4.77   22.5 2.13e-6 0.00727 AT4G… ATCAD7   
 8     8 BraA…  2.90   0.654  21.7 3.20e-6 0.00857 AT4G… AtGGCT2;2
 9     9 BraA…  0.938  7.04   21.6 3.29e-6 0.00857 AT1G… AtPMT3   
10    10 BraA… -0.865  4.13   21.5 3.59e-6 0.00857 AT5G… <NA>     
# ... with 360 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$leaf.trtdead.DEGs.int.rL.rUN.v3.0anno
# A tibble: 0 x 11
# ... with 11 variables: X1 <int>, genes <chr>, logFC <dbl>, logCPM <dbl>,
#   LR <dbl>, PValue <dbl>, FDR <dbl>, AGI <chr>, At_symbol <chr>,
#   At_short_description <chr>, perc_ID <dbl>

$leaf.trtlive_densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno
# A tibble: 63 x 12
      X1 genes logFC.trtlive logFC.densitycr… logCPM    LR  PValue     FDR
   <int> <chr>         <dbl>            <dbl>  <dbl> <dbl>   <dbl>   <dbl>
 1     1 BraA…        0.276             0.766  7.58   29.4 4.09e-7 0.00976
 2     2 BraA…        0.489             0.376  4.13   26.8 1.54e-6 0.0177 
 3     3 BraA…       -0.758            -2.15   0.654  25.6 2.74e-6 0.0177 
 4     4 BraA…       -0.189            -0.714  4.94   25.2 3.36e-6 0.0177 
 5     5 BraA…        0.0786            1.22   5.52   24.7 4.23e-6 0.0177 
 6     6 BraA…       -0.192            -0.772  4.89   24.6 4.45e-6 0.0177 
 7     7 BraA…       -0.124            -1.14   4.46   24.1 5.93e-6 0.0186 
 8     8 BraA…       -1.25              3.95   0.659  23.9 6.59e-6 0.0186 
 9     9 BraA…       -0.0242            1.70   3.11   23.5 7.77e-6 0.0186 
10    10 BraA…       -0.916             2.00   4.58   23.5 7.80e-6 0.0186 
# ... with 53 more rows, and 4 more variables: AGI <chr>, At_symbol <chr>,
#   At_short_description <chr>, perc_ID <dbl>

$leaf.trtlive_densityun.trtlive.DEGs.int.rD.rCR.v3.0anno
# A tibble: 63 x 12
      X1 genes logFC.trtlive logFC.densityun… logCPM    LR  PValue     FDR
   <int> <chr>         <dbl>            <dbl>  <dbl> <dbl>   <dbl>   <dbl>
 1     1 BraA…         1.04            -0.766  7.58   29.4 4.09e-7 0.00976
 2     2 BraA…         0.865           -0.376  4.13   26.8 1.54e-6 0.0177 
 3     3 BraA…        -2.90             2.15   0.654  25.6 2.74e-6 0.0177 
 4     4 BraA…        -0.903            0.714  4.94   25.2 3.36e-6 0.0177 
 5     5 BraA…         1.30            -1.22   5.52   24.7 4.23e-6 0.0177 
 6     6 BraA…        -0.964            0.772  4.89   24.6 4.45e-6 0.0177 
 7     7 BraA…        -1.27             1.14   4.46   24.1 5.93e-6 0.0186 
 8     8 BraA…         2.70            -3.95   0.659  23.9 6.59e-6 0.0186 
 9     9 BraA…         1.67            -1.70   3.11   23.5 7.77e-6 0.0186 
10    10 BraA…         1.09            -2.00   4.58   23.5 7.80e-6 0.0186 
# ... with 53 more rows, and 4 more variables: AGI <chr>, At_symbol <chr>,
#   At_short_description <chr>, perc_ID <dbl>

$leaf.trtlive.DEGs.add.rD.rCR.v3.0anno
# A tibble: 3 x 11
     X1 genes logFC logCPM    LR  PValue    FDR AGI   At_symbol
  <int> <chr> <dbl>  <dbl> <dbl>   <dbl>  <dbl> <chr> <chr>    
1     1 BraA… 0.702  4.13   24.5 7.56e-7 0.0181 AT5G… <NA>     
2     2 BraA… 0.599  5.50   21.2 4.08e-6 0.0375 AT5G… ORP3C    
3     3 BraA… 1.92   0.414  21.0 4.71e-6 0.0375 AT5G… <NA>     
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>

$leaf.trtlive.DEGs.add.rD.rUN.v3.0anno
# A tibble: 3 x 11
     X1 genes logFC logCPM    LR  PValue    FDR AGI   At_symbol
  <int> <chr> <dbl>  <dbl> <dbl>   <dbl>  <dbl> <chr> <chr>    
1     1 BraA… 0.702  4.13   24.5 7.56e-7 0.0181 AT5G… <NA>     
2     2 BraA… 0.599  5.50   21.2 4.08e-6 0.0375 AT5G… ORP3C    
3     3 BraA… 1.92   0.414  21.0 4.71e-6 0.0375 AT5G… <NA>     
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>

$leaf.trtlive.DEGs.int.rD.rCR.v3.0anno
# A tibble: 370 x 11
      X1 genes  logFC logCPM    LR  PValue     FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>   <dbl>   <dbl> <chr> <chr>    
 1     1 BraA…  1.04   7.58   27.5 1.57e-7 0.00374 AT5G… AtHsp90-3
 2     2 BraA…  1.30   5.52   24.7 6.80e-7 0.00491 AT2G… <NA>     
 3     3 BraA… -1.27   4.46   23.8 1.06e-6 0.00491 AT1G… HHO6     
 4     4 BraA… -0.903  4.94   23.8 1.07e-6 0.00491 AT4G… PDE327   
 5     5 BraA… -0.964  4.89   23.6 1.19e-6 0.00491 AT5G… ATFTSZ1-1
 6     6 BraA…  1.67   3.11   23.5 1.23e-6 0.00491 AT5G… <NA>     
 7     7 BraA… -0.856  4.77   22.5 2.13e-6 0.00727 AT4G… ATCAD7   
 8     8 BraA… -2.90   0.654  21.7 3.20e-6 0.00857 AT4G… AtGGCT2;2
 9     9 BraA… -0.938  7.04   21.6 3.29e-6 0.00857 AT1G… AtPMT3   
10    10 BraA…  0.865  4.13   21.5 3.59e-6 0.00857 AT5G… <NA>     
# ... with 360 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$leaf.trtlive.DEGs.int.rD.rUN.v3.0anno
# A tibble: 0 x 11
# ... with 11 variables: X1 <int>, genes <chr>, logFC <dbl>, logCPM <dbl>,
#   LR <dbl>, PValue <dbl>, FDR <dbl>, AGI <chr>, At_symbol <chr>,
#   At_short_description <chr>, perc_ID <dbl>

$leaf.un.trtlive.DEGs.all.rD.v3.0anno
# A tibble: 0 x 11
# ... with 11 variables: X1 <int>, genes <chr>, logFC <dbl>, logCPM <dbl>,
#   LR <dbl>, PValue <dbl>, FDR <dbl>, AGI <chr>, At_symbol <chr>,
#   At_short_description <chr>, perc_ID <dbl>

$root.cr.trtlive.DEGs.all.rD.v3.0anno
# A tibble: 3,887 x 11
      X1 genes  logFC logCPM    LR   PValue      FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>    <dbl>    <dbl> <chr> <chr>    
 1     1 BraA… -1.96    4.70  87.7 7.54e-21 1.07e-16 AT1G… ASP4     
 2     2 BraA…  1.22    5.63  87.6 8.17e-21 1.07e-16 AT2G… <NA>     
 3     3 BraA…  1.28    5.28  83.6 6.07e-20 5.29e-16 AT1G… BRR2     
 4     4 BraA… -1.15    5.99  81.6 1.70e-19 1.11e-15 AT2G… <NA>     
 5     5 BraA…  1.14    7.09  75.2 4.17e-18 2.18e-14 AT1G… BRR2     
 6     6 BraA…  1.02    5.44  74.1 7.24e-18 3.16e-14 AT5G… <NA>     
 7     7 BraA…  1.94    3.77  71.4 2.91e-17 1.09e-13 AT3G… TIC      
 8     8 BraA…  0.928   7.49  69.8 6.47e-17 2.03e-13 AT2G… ATGSL03  
 9     9 BraA…  1.59    3.73  69.7 6.98e-17 2.03e-13 AT1G… ASU1     
10    10 BraA…  1.30    3.72  66.9 2.79e-16 7.10e-13 AT5G… <NA>     
# ... with 3,877 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.densitycr_densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno
# A tibble: 8,708 x 12
      X1 genes logFC.densitycr logFC.densitycr… logCPM    LR    PValue
   <int> <chr>           <dbl>            <dbl>  <dbl> <dbl>     <dbl>
 1     1 BraA…           -2.88           0.498    5.32  778. 1.17e-169
 2     2 BraA…            2.50          -0.287    4.42  511. 1.05e-111
 3     3 BraA…           -3.53           1.22     6.17  491. 2.16e-107
 4     4 BraA…           -3.95           1.12     4.01  486. 2.51e-106
 5     5 BraA…           -4.44          -0.0881   4.23  454. 2.05e- 99
 6     6 BraA…           -2.58           0.467    6.28  445. 2.56e- 97
 7     7 BraA…            2.08          -0.172    7.33  441. 2.06e- 96
 8     8 BraA…            3.07           0.696    4.36  421. 4.47e- 92
 9     9 BraA…           -3.22           0.782    5.90  383. 5.42e- 84
10    10 BraA…           -2.31           0.691    4.98  375. 3.95e- 82
# ... with 8,698 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$root.densitycr_densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno
# A tibble: 8,708 x 12
      X1 genes logFC.densitycr logFC.densitycr… logCPM    LR    PValue
   <int> <chr>           <dbl>            <dbl>  <dbl> <dbl>     <dbl>
 1     1 BraA…           -2.38          -0.498    5.32  778. 1.17e-169
 2     2 BraA…            2.21           0.287    4.42  511. 1.05e-111
 3     3 BraA…           -2.31          -1.22     6.17  491. 2.16e-107
 4     4 BraA…           -2.83          -1.12     4.01  486. 2.51e-106
 5     5 BraA…           -4.53           0.0881   4.23  454. 2.05e- 99
 6     6 BraA…           -2.11          -0.467    6.28  445. 2.56e- 97
 7     7 BraA…            1.90           0.172    7.33  441. 2.06e- 96
 8     8 BraA…            3.76          -0.696    4.36  421. 4.47e- 92
 9     9 BraA…           -2.44          -0.782    5.90  383. 5.42e- 84
10    10 BraA…           -1.62          -0.691    4.98  375. 3.95e- 82
# ... with 8,698 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$root.densitycr.DEGs.add.rD.rUN.v3.0anno
# A tibble: 8,363 x 11
      X1 genes logFC logCPM    LR    PValue       FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>     <dbl>     <dbl> <chr> <chr>    
 1     1 BraA… -2.62   5.32  656. 1.22e-144 3.21e-140 AT1G… AST56    
 2     2 BraA…  2.36   4.42  494. 1.97e-109 2.60e-105 AT1G… NLP4     
 3     3 BraA… -4.48   4.23  458. 1.38e-101 1.22e- 97 AT3G… ATIPT3   
 4     4 BraA…  1.99   7.33  436. 9.96e- 97 6.56e- 93 AT5G… AAP2     
 5     5 BraA… -2.34   6.28  395. 6.92e- 88 3.65e- 84 AT1G… ATTPPB   
 6     6 BraA…  3.38   4.35  370. 2.32e- 82 1.02e- 78 AT5G… <NA>     
 7     7 BraA…  6.68   3.06  368. 5.13e- 82 1.93e- 78 AT3G… NLP9     
 8     8 BraA… -2.47   5.28  358. 9.38e- 80 3.09e- 76 AT1G… ATATP-PR…
 9     9 BraA…  2.81   4.13  342. 1.82e- 76 5.33e- 73 AT5G… <NA>     
10    10 BraA… -3.34   4.01  336. 4.16e- 75 1.04e- 71 AT5G… <NA>     
# ... with 8,353 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.densitycr.DEGs.add.rL.rUN.v3.0anno
# A tibble: 8,363 x 11
      X1 genes logFC logCPM    LR    PValue       FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>     <dbl>     <dbl> <chr> <chr>    
 1     1 BraA… -2.62   5.32  656. 1.22e-144 3.21e-140 AT1G… AST56    
 2     2 BraA…  2.36   4.42  494. 1.97e-109 2.60e-105 AT1G… NLP4     
 3     3 BraA… -4.48   4.23  458. 1.38e-101 1.22e- 97 AT3G… ATIPT3   
 4     4 BraA…  1.99   7.33  436. 9.96e- 97 6.56e- 93 AT5G… AAP2     
 5     5 BraA… -2.34   6.28  395. 6.92e- 88 3.65e- 84 AT1G… ATTPPB   
 6     6 BraA…  3.38   4.35  370. 2.32e- 82 1.02e- 78 AT5G… <NA>     
 7     7 BraA…  6.68   3.06  368. 5.13e- 82 1.93e- 78 AT3G… NLP9     
 8     8 BraA… -2.47   5.28  358. 9.38e- 80 3.09e- 76 AT1G… ATATP-PR…
 9     9 BraA…  2.81   4.13  342. 1.82e- 76 5.33e- 73 AT5G… <NA>     
10    10 BraA… -3.34   4.01  336. 4.16e- 75 1.04e- 71 AT5G… <NA>     
# ... with 8,353 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno
# A tibble: 471 x 11
      X1 genes logFC logCPM    LR   PValue     FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>    <dbl>   <dbl> <chr> <chr>    
 1     1 BraA…  2.06  4.03   41.3 1.28e-10 3.36e-6 AT3G… BHLH039  
 2     2 BraA…  1.60  5.88   36.8 1.33e- 9 1.75e-5 AT1G… ASP4     
 3     3 BraA…  1.11  6.78   32.4 1.27e- 8 1.12e-4 AT1G… ATSBT5.2 
 4     4 BraA…  3.40  5.12   28.1 1.13e- 7 7.45e-4 AT3G… <NA>     
 5     5 BraA…  1.50  4.22   26.7 2.33e- 7 1.14e-3 AT4G… ATIRT1   
 6     6 BraA…  3.19  2.39   26.5 2.60e- 7 1.14e-3 AT1G… GAT      
 7     7 BraA…  3.72  0.831  24.9 6.10e- 7 2.10e-3 AT5G… <NA>     
 8     8 BraA…  1.72  5.26   24.8 6.39e- 7 2.10e-3 AT5G… AtCOMT   
 9     9 BraA…  2.14  5.04   24.0 9.43e- 7 2.76e-3 AT3G… F6'H1    
10    10 BraA…  1.84  4.05   23.8 1.08e- 6 2.84e-3 AT4G… <NA>     
# ... with 461 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno
# A tibble: 471 x 11
      X1 genes logFC logCPM    LR   PValue     FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>    <dbl>   <dbl> <chr> <chr>    
 1     1 BraA… -2.06  4.03   41.3 1.28e-10 3.36e-6 AT3G… BHLH039  
 2     2 BraA… -1.60  5.88   36.8 1.33e- 9 1.75e-5 AT1G… ASP4     
 3     3 BraA… -1.11  6.78   32.4 1.27e- 8 1.12e-4 AT1G… ATSBT5.2 
 4     4 BraA… -3.40  5.12   28.1 1.13e- 7 7.45e-4 AT3G… <NA>     
 5     5 BraA… -1.50  4.22   26.7 2.33e- 7 1.14e-3 AT4G… ATIRT1   
 6     6 BraA… -3.19  2.39   26.5 2.60e- 7 1.14e-3 AT1G… GAT      
 7     7 BraA… -3.72  0.831  24.9 6.10e- 7 2.10e-3 AT5G… <NA>     
 8     8 BraA… -1.72  5.26   24.8 6.39e- 7 2.10e-3 AT5G… AtCOMT   
 9     9 BraA… -2.14  5.04   24.0 9.43e- 7 2.76e-3 AT3G… F6'H1    
10    10 BraA… -1.84  4.05   23.8 1.08e- 6 2.84e-3 AT4G… <NA>     
# ... with 461 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.densityun_densityun.trtdead.DEGs.int.rL.rCR.v3.0anno
# A tibble: 8,708 x 12
      X1 genes logFC.densityun logFC.densityun… logCPM    LR    PValue
   <int> <chr>           <dbl>            <dbl>  <dbl> <dbl>     <dbl>
 1     1 BraA…            2.88          -0.498    5.32  778. 1.17e-169
 2     2 BraA…           -2.50           0.287    4.42  511. 1.05e-111
 3     3 BraA…            3.53          -1.22     6.17  491. 2.16e-107
 4     4 BraA…            3.95          -1.12     4.01  486. 2.51e-106
 5     5 BraA…            4.44           0.0881   4.23  454. 2.05e- 99
 6     6 BraA…            2.58          -0.467    6.28  445. 2.56e- 97
 7     7 BraA…           -2.08           0.172    7.33  441. 2.06e- 96
 8     8 BraA…           -3.07          -0.696    4.36  421. 4.47e- 92
 9     9 BraA…            3.22          -0.782    5.90  383. 5.42e- 84
10    10 BraA…            2.31          -0.691    4.98  375. 3.95e- 82
# ... with 8,698 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$root.densityun_densityun.trtlive.DEGs.int.rD.rCR.v3.0anno
# A tibble: 8,708 x 12
      X1 genes logFC.densityun logFC.densityun… logCPM    LR    PValue
   <int> <chr>           <dbl>            <dbl>  <dbl> <dbl>     <dbl>
 1     1 BraA…            2.38           0.498    5.32  778. 1.17e-169
 2     2 BraA…           -2.21          -0.287    4.42  511. 1.05e-111
 3     3 BraA…            2.31           1.22     6.17  491. 2.16e-107
 4     4 BraA…            2.83           1.12     4.01  486. 2.51e-106
 5     5 BraA…            4.53          -0.0881   4.23  454. 2.05e- 99
 6     6 BraA…            2.11           0.467    6.28  445. 2.56e- 97
 7     7 BraA…           -1.90          -0.172    7.33  441. 2.06e- 96
 8     8 BraA…           -3.76           0.696    4.36  421. 4.47e- 92
 9     9 BraA…            2.44           0.782    5.90  383. 5.42e- 84
10    10 BraA…            1.62           0.691    4.98  375. 3.95e- 82
# ... with 8,698 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$root.densityun.DEGs.add.rD.rCR.v3.0anno
# A tibble: 8,363 x 11
      X1 genes logFC logCPM    LR    PValue       FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>     <dbl>     <dbl> <chr> <chr>    
 1     1 BraA…  2.62   5.32  656. 1.22e-144 3.21e-140 AT1G… AST56    
 2     2 BraA… -2.36   4.42  494. 1.97e-109 2.60e-105 AT1G… NLP4     
 3     3 BraA…  4.48   4.23  458. 1.38e-101 1.22e- 97 AT3G… ATIPT3   
 4     4 BraA… -1.99   7.33  436. 9.96e- 97 6.56e- 93 AT5G… AAP2     
 5     5 BraA…  2.34   6.28  395. 6.92e- 88 3.65e- 84 AT1G… ATTPPB   
 6     6 BraA… -3.38   4.35  370. 2.32e- 82 1.02e- 78 AT5G… <NA>     
 7     7 BraA… -6.68   3.06  368. 5.13e- 82 1.93e- 78 AT3G… NLP9     
 8     8 BraA…  2.47   5.28  358. 9.38e- 80 3.09e- 76 AT1G… ATATP-PR…
 9     9 BraA… -2.81   4.13  342. 1.82e- 76 5.33e- 73 AT5G… <NA>     
10    10 BraA…  3.34   4.01  336. 4.16e- 75 1.04e- 71 AT5G… <NA>     
# ... with 8,353 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.densityun.DEGs.add.rL.rCR.v3.0anno
# A tibble: 8,363 x 11
      X1 genes logFC logCPM    LR    PValue       FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>     <dbl>     <dbl> <chr> <chr>    
 1     1 BraA…  2.62   5.32  656. 1.22e-144 3.21e-140 AT1G… AST56    
 2     2 BraA… -2.36   4.42  494. 1.97e-109 2.60e-105 AT1G… NLP4     
 3     3 BraA…  4.48   4.23  458. 1.38e-101 1.22e- 97 AT3G… ATIPT3   
 4     4 BraA… -1.99   7.33  436. 9.96e- 97 6.56e- 93 AT5G… AAP2     
 5     5 BraA…  2.34   6.28  395. 6.92e- 88 3.65e- 84 AT1G… ATTPPB   
 6     6 BraA… -3.38   4.35  370. 2.32e- 82 1.02e- 78 AT5G… <NA>     
 7     7 BraA… -6.68   3.06  368. 5.13e- 82 1.93e- 78 AT3G… NLP9     
 8     8 BraA…  2.47   5.28  358. 9.38e- 80 3.09e- 76 AT1G… ATATP-PR…
 9     9 BraA… -2.81   4.13  342. 1.82e- 76 5.33e- 73 AT5G… <NA>     
10    10 BraA…  3.34   4.01  336. 4.16e- 75 1.04e- 71 AT5G… <NA>     
# ... with 8,353 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.densityun.trtdead.DEGs.int.rL.rCR.v3.0anno
# A tibble: 471 x 12
      X1 genes logFC logCPM    LR   PValue     FDR  X1_1 AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>    <dbl>   <dbl> <int> <chr> <chr>    
 1     1 BraA… -2.06  4.03   41.3 1.28e-10 3.36e-6 15390 AT3G… BHLH039  
 2     2 BraA… -1.60  5.88   36.8 1.33e- 9 1.75e-5 35547 AT1G… ASP4     
 3     3 BraA… -1.11  6.78   32.4 1.27e- 8 1.12e-4 23863 AT1G… ATSBT5.2 
 4     4 BraA… -3.40  5.12   28.1 1.13e- 7 7.45e-4  4032 AT3G… <NA>     
 5     5 BraA… -1.50  4.22   26.7 2.33e- 7 1.14e-3  1149 AT4G… ATIRT1   
 6     6 BraA… -3.19  2.39   26.5 2.60e- 7 1.14e-3 39482 AT1G… GAT      
 7     7 BraA… -3.72  0.831  24.9 6.10e- 7 2.10e-3 28198 AT5G… <NA>     
 8     8 BraA… -1.72  5.26   24.8 6.39e- 7 2.10e-3 14171 AT5G… AtCOMT   
 9     9 BraA… -2.14  5.04   24.0 9.43e- 7 2.76e-3 21279 AT3G… F6'H1    
10    10 BraA… -1.84  4.05   23.8 1.08e- 6 2.84e-3   771 AT4G… <NA>     
# ... with 461 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.densityun.trtlive.DEGs.int.rD.rCR.v3.0anno
# A tibble: 471 x 11
      X1 genes logFC logCPM    LR   PValue     FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>    <dbl>   <dbl> <chr> <chr>    
 1     1 BraA…  2.06  4.03   41.3 1.28e-10 3.36e-6 AT3G… BHLH039  
 2     2 BraA…  1.60  5.88   36.8 1.33e- 9 1.75e-5 AT1G… ASP4     
 3     3 BraA…  1.11  6.78   32.4 1.27e- 8 1.12e-4 AT1G… ATSBT5.2 
 4     4 BraA…  3.40  5.12   28.1 1.13e- 7 7.45e-4 AT3G… <NA>     
 5     5 BraA…  1.50  4.22   26.7 2.33e- 7 1.14e-3 AT4G… ATIRT1   
 6     6 BraA…  3.19  2.39   26.5 2.60e- 7 1.14e-3 AT1G… GAT      
 7     7 BraA…  3.72  0.831  24.9 6.10e- 7 2.10e-3 AT5G… <NA>     
 8     8 BraA…  1.72  5.26   24.8 6.39e- 7 2.10e-3 AT5G… AtCOMT   
 9     9 BraA…  2.14  5.04   24.0 9.43e- 7 2.76e-3 AT3G… F6'H1    
10    10 BraA…  1.84  4.05   23.8 1.08e- 6 2.84e-3 AT4G… <NA>     
# ... with 461 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.trtdead_densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno
# A tibble: 3,857 x 12
      X1 genes logFC.trtdead logFC.densitycr… logCPM    LR   PValue
   <int> <chr>         <dbl>            <dbl>  <dbl> <dbl>    <dbl>
 1     1 BraA…        0.370             1.60    5.88 105.  1.40e-23
 2     2 BraA…        0.0552            2.06    4.03  77.8 1.27e-17
 3     3 BraA…        0.372             0.682   6.91  73.4 1.16e-16
 4     4 BraA…        0.211             1.50    4.22  65.5 5.99e-15
 5     5 BraA…       -0.523            -0.132   8.54  63.6 1.56e-14
 6     6 BraA…       -0.331            -0.590   7.24  60.6 6.97e-14
 7     7 BraA…       -2.20              1.84    2.44  59.1 1.50e-13
 8     8 BraA…       -2.52              1.41    1.76  58.1 2.36e-13
 9     9 BraA…       -0.128            -0.895   5.25  56.8 4.62e-13
10    10 BraA…       -0.231            -0.989   5.48  55.3 9.90e-13
# ... with 3,847 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$root.trtdead_densityun.trtdead.DEGs.int.rL.rCR.v3.0anno
# A tibble: 3,857 x 12
      X1 genes logFC.trtdead logFC.densityun… logCPM    LR   PValue
   <int> <chr>         <dbl>            <dbl>  <dbl> <dbl>    <dbl>
 1     1 BraA…         1.97            -1.60    5.88 105.  1.40e-23
 2     2 BraA…         2.11            -2.06    4.03  77.8 1.27e-17
 3     3 BraA…         1.05            -0.682   6.91  73.4 1.16e-16
 4     4 BraA…         1.71            -1.50    4.22  65.5 5.99e-15
 5     5 BraA…        -0.655            0.132   8.54  63.6 1.56e-14
 6     6 BraA…        -0.921            0.590   7.24  60.6 6.97e-14
 7     7 BraA…        -0.353           -1.84    2.44  59.1 1.50e-13
 8     8 BraA…        -1.12            -1.41    1.76  58.1 2.36e-13
 9     9 BraA…        -1.02             0.895   5.25  56.8 4.62e-13
10    10 BraA…        -1.22             0.989   5.48  55.3 9.90e-13
# ... with 3,847 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$root.trtdead.DEGs.add.rL.rCR.v3.0anno
# A tibble: 3,352 x 11
      X1 genes  logFC logCPM    LR   PValue      FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>    <dbl>    <dbl> <chr> <chr>    
 1     1 BraA… -0.590   8.54  62.3 2.94e-15 7.74e-11 AT2G… ATUBC24  
 2     2 BraA…  2.18    1.59  55.7 8.55e-14 1.13e- 9 AT2G… <NA>     
 3     3 BraA…  1.10    2.65  49.2 2.27e-12 1.99e- 8 AT1G… <NA>     
 4     4 BraA…  0.482   6.84  46.0 1.17e-11 7.35e- 8 AT4G… <NA>     
 5     5 BraA… -1.61    1.61  45.3 1.67e-11 7.35e- 8 AT1G… IGMT2    
 6     6 BraA…  0.607   5.95  45.3 1.68e-11 7.35e- 8 AT2G… ATGSTU4  
 7     7 BraA… -0.528   6.88  44.9 2.07e-11 7.35e- 8 AT1G… ABCG35   
 8     8 BraA… -0.499   7.51  44.8 2.23e-11 7.35e- 8 AT1G… FB       
 9     9 BraA…  0.714   6.91  44.0 3.36e-11 9.82e- 8 AT1G… ATOPR2   
10    10 BraA… -0.569   6.15  43.5 4.27e-11 1.13e- 7 AT5G… CLPD     
# ... with 3,342 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.trtdead.DEGs.add.rL.rUN.v3.0anno
# A tibble: 3,352 x 11
      X1 genes  logFC logCPM    LR   PValue      FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>    <dbl>    <dbl> <chr> <chr>    
 1     1 BraA… -0.590   8.54  62.3 2.94e-15 7.74e-11 AT2G… ATUBC24  
 2     2 BraA…  2.18    1.59  55.7 8.55e-14 1.13e- 9 AT2G… <NA>     
 3     3 BraA…  1.10    2.65  49.2 2.27e-12 1.99e- 8 AT1G… <NA>     
 4     4 BraA…  0.482   6.84  46.0 1.17e-11 7.35e- 8 AT4G… <NA>     
 5     5 BraA… -1.61    1.61  45.3 1.67e-11 7.35e- 8 AT1G… IGMT2    
 6     6 BraA…  0.607   5.95  45.3 1.68e-11 7.35e- 8 AT2G… ATGSTU4  
 7     7 BraA… -0.528   6.88  44.9 2.07e-11 7.35e- 8 AT1G… ABCG35   
 8     8 BraA… -0.499   7.51  44.8 2.23e-11 7.35e- 8 AT1G… FB       
 9     9 BraA…  0.714   6.91  44.0 3.36e-11 9.82e- 8 AT1G… ATOPR2   
10    10 BraA… -0.569   6.15  43.5 4.27e-11 1.13e- 7 AT5G… CLPD     
# ... with 3,342 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.trtdead.DEGs.int.rL.rCR.v3.0anno
# A tibble: 3,434 x 11
      X1 genes  logFC logCPM    LR   PValue      FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>    <dbl>    <dbl> <chr> <chr>    
 1     1 BraA…  1.97    5.88 101.  9.26e-24 2.44e-19 AT1G… ASP4     
 2     2 BraA…  2.11    4.03  77.7 1.18e-18 1.55e-14 AT3G… BHLH039  
 3     3 BraA…  1.05    6.91  65.1 7.00e-16 6.15e-12 AT1G… ATOPR2   
 4     4 BraA…  1.71    4.22  64.3 1.05e-15 6.92e-12 AT4G… ATIRT1   
 5     5 BraA… -1.02    5.25  55.9 7.52e-14 3.96e-10 AT5G… <NA>     
 6     6 BraA… -0.921   7.24  53.6 2.47e-13 1.07e- 9 AT2G… ATGSL03  
 7     7 BraA… -1.22    5.48  53.3 2.83e-13 1.07e- 9 AT2G… <NA>     
 8     8 BraA…  1.81    5.26  51.7 6.49e-13 2.14e- 9 AT5G… AtCOMT   
 9     9 BraA…  1.16    5.96  50.9 9.52e-13 2.30e- 9 AT2G… <NA>     
10    10 BraA… -1.24    3.91  50.9 9.83e-13 2.30e- 9 AT4G… ATSPS4F  
# ... with 3,424 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.trtdead.DEGs.int.rL.rUN.v3.0anno
# A tibble: 357 x 11
      X1 genes  logFC logCPM    LR   PValue      FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>    <dbl>    <dbl> <chr> <chr>    
 1     1 BraA… -2.20   2.44   57.3 3.75e-14 9.87e-10 AT1G… ATGSTU12 
 2     2 BraA… -2.52   1.76   47.1 6.73e-12 7.82e- 8 AT2G… ATWRKY59 
 3     3 BraA… -4.03   0.831  46.6 8.91e-12 7.82e- 8 AT5G… <NA>     
 4     4 BraA… -1.40   3.53   41.0 1.52e-10 1.00e- 6 AT1G… HMS      
 5     5 BraA… -1.35   2.35   38.1 6.87e-10 3.27e- 6 AT2G… ANAC042  
 6     6 BraA… -2.08   3.27   37.9 7.45e-10 3.27e- 6 AT2G… <NA>     
 7     7 BraA… -1.97   5.83   34.1 5.13e- 9 1.93e- 5 AT4G… <NA>     
 8     8 BraA… -0.925  4.26   32.6 1.15e- 8 3.70e- 5 AT4G… CYP706A1 
 9     9 BraA… -1.86   2.87   32.4 1.26e- 8 3.70e- 5 AT2G… ANAC042  
10    10 BraA… -1.90   1.61   31.8 1.70e- 8 4.47e- 5 AT1G… IGMT2    
# ... with 347 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.trtlive_densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno
# A tibble: 3,857 x 12
      X1 genes logFC.trtlive logFC.densitycr… logCPM    LR   PValue
   <int> <chr>         <dbl>            <dbl>  <dbl> <dbl>    <dbl>
 1     1 BraA…       -0.370            -1.60    5.88 105.  1.40e-23
 2     2 BraA…       -0.0552           -2.06    4.03  77.8 1.27e-17
 3     3 BraA…       -0.372            -0.682   6.91  73.4 1.16e-16
 4     4 BraA…       -0.211            -1.50    4.22  65.5 5.99e-15
 5     5 BraA…        0.523             0.132   8.54  63.6 1.56e-14
 6     6 BraA…        0.331             0.590   7.24  60.6 6.97e-14
 7     7 BraA…        2.20             -1.84    2.44  59.1 1.50e-13
 8     8 BraA…        2.52             -1.41    1.76  58.1 2.36e-13
 9     9 BraA…        0.128             0.895   5.25  56.8 4.62e-13
10    10 BraA…        0.231             0.989   5.48  55.3 9.90e-13
# ... with 3,847 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$root.trtlive_densityun.trtlive.DEGs.int.rD.rCR.v3.0anno
# A tibble: 3,857 x 12
      X1 genes logFC.trtlive logFC.densityun… logCPM    LR   PValue
   <int> <chr>         <dbl>            <dbl>  <dbl> <dbl>    <dbl>
 1     1 BraA…        -1.97             1.60    5.88 105.  1.40e-23
 2     2 BraA…        -2.11             2.06    4.03  77.8 1.27e-17
 3     3 BraA…        -1.05             0.682   6.91  73.4 1.16e-16
 4     4 BraA…        -1.71             1.50    4.22  65.5 5.99e-15
 5     5 BraA…         0.655           -0.132   8.54  63.6 1.56e-14
 6     6 BraA…         0.921           -0.590   7.24  60.6 6.97e-14
 7     7 BraA…         0.353            1.84    2.44  59.1 1.50e-13
 8     8 BraA…         1.12             1.41    1.76  58.1 2.36e-13
 9     9 BraA…         1.02            -0.895   5.25  56.8 4.62e-13
10    10 BraA…         1.22            -0.989   5.48  55.3 9.90e-13
# ... with 3,847 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$root.trtlive.DEGs.add.rD.rCR.v3.0anno
# A tibble: 3,352 x 11
      X1 genes  logFC logCPM    LR   PValue      FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>    <dbl>    <dbl> <chr> <chr>    
 1     1 BraA…  0.590   8.54  62.3 2.94e-15 7.74e-11 AT2G… ATUBC24  
 2     2 BraA… -2.18    1.59  55.7 8.55e-14 1.13e- 9 AT2G… <NA>     
 3     3 BraA… -1.10    2.65  49.2 2.27e-12 1.99e- 8 AT1G… <NA>     
 4     4 BraA… -0.482   6.84  46.0 1.17e-11 7.35e- 8 AT4G… <NA>     
 5     5 BraA…  1.61    1.61  45.3 1.67e-11 7.35e- 8 AT1G… IGMT2    
 6     6 BraA… -0.607   5.95  45.3 1.68e-11 7.35e- 8 AT2G… ATGSTU4  
 7     7 BraA…  0.528   6.88  44.9 2.07e-11 7.35e- 8 AT1G… ABCG35   
 8     8 BraA…  0.499   7.51  44.8 2.23e-11 7.35e- 8 AT1G… FB       
 9     9 BraA… -0.714   6.91  44.0 3.36e-11 9.82e- 8 AT1G… ATOPR2   
10    10 BraA…  0.569   6.15  43.5 4.27e-11 1.13e- 7 AT5G… CLPD     
# ... with 3,342 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.trtlive.DEGs.add.rD.rUN.v3.0anno
# A tibble: 3,352 x 11
      X1 genes  logFC logCPM    LR   PValue      FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>    <dbl>    <dbl> <chr> <chr>    
 1     1 BraA…  0.590   8.54  62.3 2.94e-15 7.74e-11 AT2G… ATUBC24  
 2     2 BraA… -2.18    1.59  55.7 8.55e-14 1.13e- 9 AT2G… <NA>     
 3     3 BraA… -1.10    2.65  49.2 2.27e-12 1.99e- 8 AT1G… <NA>     
 4     4 BraA… -0.482   6.84  46.0 1.17e-11 7.35e- 8 AT4G… <NA>     
 5     5 BraA…  1.61    1.61  45.3 1.67e-11 7.35e- 8 AT1G… IGMT2    
 6     6 BraA… -0.607   5.95  45.3 1.68e-11 7.35e- 8 AT2G… ATGSTU4  
 7     7 BraA…  0.528   6.88  44.9 2.07e-11 7.35e- 8 AT1G… ABCG35   
 8     8 BraA…  0.499   7.51  44.8 2.23e-11 7.35e- 8 AT1G… FB       
 9     9 BraA… -0.714   6.91  44.0 3.36e-11 9.82e- 8 AT1G… ATOPR2   
10    10 BraA…  0.569   6.15  43.5 4.27e-11 1.13e- 7 AT5G… CLPD     
# ... with 3,342 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.trtlive.DEGs.int.rD.rCR.v3.0anno
# A tibble: 3,434 x 11
      X1 genes  logFC logCPM    LR   PValue      FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>    <dbl>    <dbl> <chr> <chr>    
 1     1 BraA… -1.97    5.88 101.  9.26e-24 2.44e-19 AT1G… ASP4     
 2     2 BraA… -2.11    4.03  77.7 1.18e-18 1.55e-14 AT3G… BHLH039  
 3     3 BraA… -1.05    6.91  65.1 7.00e-16 6.15e-12 AT1G… ATOPR2   
 4     4 BraA… -1.71    4.22  64.3 1.05e-15 6.92e-12 AT4G… ATIRT1   
 5     5 BraA…  1.02    5.25  55.9 7.52e-14 3.96e-10 AT5G… <NA>     
 6     6 BraA…  0.921   7.24  53.6 2.47e-13 1.07e- 9 AT2G… ATGSL03  
 7     7 BraA…  1.22    5.48  53.3 2.83e-13 1.07e- 9 AT2G… <NA>     
 8     8 BraA… -1.81    5.26  51.7 6.49e-13 2.14e- 9 AT5G… AtCOMT   
 9     9 BraA… -1.16    5.96  50.9 9.52e-13 2.30e- 9 AT2G… <NA>     
10    10 BraA…  1.24    3.91  50.9 9.83e-13 2.30e- 9 AT4G… ATSPS4F  
# ... with 3,424 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.trtlive.DEGs.int.rD.rUN.v3.0anno
# A tibble: 357 x 11
      X1 genes logFC logCPM    LR   PValue      FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>    <dbl>    <dbl> <chr> <chr>    
 1     1 BraA… 2.20   2.44   57.3 3.75e-14 9.87e-10 AT1G… ATGSTU12 
 2     2 BraA… 2.52   1.76   47.1 6.73e-12 7.82e- 8 AT2G… ATWRKY59 
 3     3 BraA… 4.03   0.831  46.6 8.91e-12 7.82e- 8 AT5G… <NA>     
 4     4 BraA… 1.40   3.53   41.0 1.52e-10 1.00e- 6 AT1G… HMS      
 5     5 BraA… 1.35   2.35   38.1 6.87e-10 3.27e- 6 AT2G… ANAC042  
 6     6 BraA… 2.08   3.27   37.9 7.45e-10 3.27e- 6 AT2G… <NA>     
 7     7 BraA… 1.97   5.83   34.1 5.13e- 9 1.93e- 5 AT4G… <NA>     
 8     8 BraA… 0.925  4.26   32.6 1.15e- 8 3.70e- 5 AT4G… CYP706A1 
 9     9 BraA… 1.86   2.87   32.4 1.26e- 8 3.70e- 5 AT2G… ANAC042  
10    10 BraA… 1.90   1.61   31.8 1.70e- 8 4.47e- 5 AT1G… IGMT2    
# ... with 347 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.un.trtlive.DEGs.all.rD.v3.0anno
# A tibble: 297 x 11
      X1 genes  logFC logCPM    LR   PValue     FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>    <dbl>   <dbl> <chr> <chr>    
 1     1 BraA…  2.19   2.37   56.7 5.00e-14 1.30e-9 AT1G… ATGSTU12 
 2     2 BraA…  2.06   3.30   47.4 5.87e-12 5.83e-8 AT2G… <NA>     
 3     3 BraA…  4.05   0.567  47.1 6.75e-12 5.83e-8 AT5G… <NA>     
 4     4 BraA…  2.52   1.68   46.1 1.13e-11 7.29e-8 AT2G… ATWRKY59 
 5     5 BraA… -2.17   1.80   45.7 1.41e-11 7.32e-8 AT2G… <NA>     
 6     6 BraA…  1.41   2.87   43.4 4.55e-11 1.97e-7 AT1G… HMS      
 7     7 BraA…  1.86   2.20   38.3 5.95e-10 2.20e-6 AT2G… ANAC042  
 8     8 BraA…  0.933  4.20   38.0 7.03e-10 2.28e-6 AT4G… CYP706A1 
 9     9 BraA…  1.46   1.59   37.5 9.38e-10 2.70e-6 AT5G… <NA>     
10    10 BraA…  1.90   1.67   36.6 1.48e- 9 3.84e-6 AT1G… IGMT2    
# ... with 287 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>
lapply(DEG.count.list.e3.v3.0annotation.all,function(df) filter(df,FDR<0.05)) # does work
$leaf.cr.trtlive.DEGs.all.rD.v3.0anno
# A tibble: 12 x 11
      X1 genes  logFC logCPM    LR  PValue    FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>   <dbl>  <dbl> <chr> <chr>    
 1     1 BraA…  2.75   2.86   20.6 5.77e-6 0.0413 AT1G… <NA>     
 2     2 BraA…  1.05   8.17   19.2 1.19e-5 0.0413 AT5G… AtHsp90-3
 3     3 BraA… -3.07   0.296  18.7 1.49e-5 0.0413 AT2G… PLAT2    
 4     4 BraA…  2.69   0.508  18.7 1.50e-5 0.0413 AT1G… <NA>     
 5     5 BraA… -0.961  7.30   18.7 1.51e-5 0.0413 AT1G… AtPMT3   
 6     6 BraA…  1.64   3.71   18.7 1.51e-5 0.0413 AT5G… AAP4     
 7     7 BraA…  1.66   2.15   18.7 1.54e-5 0.0413 AT2G… ArathEUL…
 8     8 BraA… -0.846  4.97   18.5 1.71e-5 0.0413 AT4G… ATCAD7   
 9     9 BraA…  1.68   3.95   18.3 1.89e-5 0.0413 AT5G… <NA>     
10    10 BraA…  2.83   1.000  18.3 1.91e-5 0.0413 AT5G… ANAC092  
11    11 BraA…  2.35   2.04   18.2 1.94e-5 0.0413 AT5G… <NA>     
12    12 BraA…  1.67   2.20   17.8 2.40e-5 0.0469 AT5G… <NA>     
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>

$leaf.densitycr_densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno
# A tibble: 14,074 x 12
      X1 genes logFC.densitycr logFC.densitycr… logCPM    LR    PValue
   <int> <chr>           <dbl>            <dbl>  <dbl> <dbl>     <dbl>
 1     1 BraA…           -7.74          1.09      4.09  891. 2.88e-194
 2     2 BraA…           -2.65          0.0205    8.15  664. 7.63e-145
 3     3 BraA…           -2.66         -0.00762   7.37  574. 1.78e-125
 4     4 BraA…            3.98          0.267     7.24  510. 1.56e-111
 5     5 BraA…           -4.47          0.399     7.29  494. 6.31e-108
 6     6 BraA…           -2.65          0.139     7.53  491. 1.88e-107
 7     7 BraA…           -2.11         -0.281     6.87  477. 2.91e-104
 8     8 BraA…           -3.09          0.124     5.97  471. 5.85e-103
 9     9 BraA…           -3.07         -0.179     7.57  470. 7.61e-103
10    10 BraA…           -2.45         -0.0962    4.91  467. 3.40e-102
# ... with 14,064 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$leaf.densitycr_densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno
# A tibble: 14,074 x 12
      X1 genes logFC.densitycr logFC.densitycr… logCPM    LR    PValue
   <int> <chr>           <dbl>            <dbl>  <dbl> <dbl>     <dbl>
 1     1 BraA…           -6.65         -1.09      4.09  891. 2.88e-194
 2     2 BraA…           -2.63         -0.0205    8.15  664. 7.63e-145
 3     3 BraA…           -2.67          0.00762   7.37  574. 1.78e-125
 4     4 BraA…            4.25         -0.267     7.24  510. 1.56e-111
 5     5 BraA…           -4.07         -0.399     7.29  494. 6.31e-108
 6     6 BraA…           -2.51         -0.139     7.53  491. 1.88e-107
 7     7 BraA…           -2.39          0.281     6.87  477. 2.91e-104
 8     8 BraA…           -2.97         -0.124     5.97  471. 5.85e-103
 9     9 BraA…           -3.25          0.179     7.57  470. 7.61e-103
10    10 BraA…           -2.55          0.0962    4.91  467. 3.40e-102
# ... with 14,064 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$leaf.densitycr.DEGs.add.rD.rUN.v3.0anno
# A tibble: 14,919 x 11
      X1 genes logFC logCPM    LR    PValue       FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>     <dbl>     <dbl> <chr> <chr>    
 1     1 BraA… -7.03   4.09  860. 5.16e-189 1.23e-184 AT1G… ARR4     
 2     2 BraA… -2.64   8.15  678. 1.81e-149 2.16e-145 AT5G… RPL4     
 3     3 BraA… -2.67   7.37  588. 6.29e-130 5.01e-126 AT1G… ARP1     
 4     4 BraA…  4.11   7.24  512. 2.09e-113 1.25e-109 AT5G… <NA>     
 5     5 BraA… -2.58   7.53  497. 3.90e-110 1.86e-106 AT4G… HLN      
 6     6 BraA… -4.26   7.29  485. 1.51e-107 6.00e-104 AT5G… ATHD2    
 7     7 BraA… -3.03   5.97  480. 1.91e-106 6.52e-103 AT3G… <NA>     
 8     8 BraA… -2.50   4.91  478. 6.82e-106 2.04e-102 AT2G… ASHR2    
 9     9 BraA… -3.16   7.57  475. 2.11e-105 5.60e-102 AT5G… ATHD2    
10    10 BraA… -2.25   6.87  460. 5.80e-102 1.39e- 98 AT5G… NAP1;3   
# ... with 14,909 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$leaf.densitycr.DEGs.add.rL.rUN.v3.0anno
# A tibble: 14,919 x 11
      X1 genes logFC logCPM    LR    PValue       FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>     <dbl>     <dbl> <chr> <chr>    
 1     1 BraA… -7.03   4.09  860. 5.16e-189 1.23e-184 AT1G… ARR4     
 2     2 BraA… -2.64   8.15  678. 1.81e-149 2.16e-145 AT5G… RPL4     
 3     3 BraA… -2.67   7.37  588. 6.29e-130 5.01e-126 AT1G… ARP1     
 4     4 BraA…  4.11   7.24  512. 2.09e-113 1.25e-109 AT5G… <NA>     
 5     5 BraA… -2.58   7.53  497. 3.90e-110 1.86e-106 AT4G… HLN      
 6     6 BraA… -4.26   7.29  485. 1.51e-107 6.00e-104 AT5G… ATHD2    
 7     7 BraA… -3.03   5.97  480. 1.91e-106 6.52e-103 AT3G… <NA>     
 8     8 BraA… -2.50   4.91  478. 6.82e-106 2.04e-102 AT2G… ASHR2    
 9     9 BraA… -3.16   7.57  475. 2.11e-105 5.60e-102 AT5G… ATHD2    
10    10 BraA… -2.25   6.87  460. 5.80e-102 1.39e- 98 AT5G… NAP1;3   
# ... with 14,909 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$leaf.densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno
# A tibble: 2 x 11
     X1 genes logFC logCPM    LR  PValue    FDR AGI   At_symbol
  <int> <chr> <dbl>  <dbl> <dbl>   <dbl>  <dbl> <chr> <chr>    
1     1 BraA… -2.00  4.58   22.9 1.69e-6 0.0271 AT1G… ARR7     
2     2 BraA… -3.95  0.659  22.3 2.27e-6 0.0271 AT1G… <NA>     
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>

$leaf.densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno
# A tibble: 2 x 11
     X1 genes logFC logCPM    LR  PValue    FDR AGI   At_symbol
  <int> <chr> <dbl>  <dbl> <dbl>   <dbl>  <dbl> <chr> <chr>    
1     1 BraA…  2.00  4.58   22.9 1.69e-6 0.0271 AT1G… ARR7     
2     2 BraA…  3.95  0.659  22.3 2.27e-6 0.0271 AT1G… <NA>     
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>

$leaf.densityun_densityun.trtdead.DEGs.int.rL.rCR.v3.0anno
# A tibble: 14,074 x 12
      X1 genes logFC.densityun logFC.densityun… logCPM    LR    PValue
   <int> <chr>           <dbl>            <dbl>  <dbl> <dbl>     <dbl>
 1     1 BraA…            7.74         -1.09      4.09  891. 2.88e-194
 2     2 BraA…            2.65         -0.0205    8.15  664. 7.63e-145
 3     3 BraA…            2.66          0.00762   7.37  574. 1.78e-125
 4     4 BraA…           -3.98         -0.267     7.24  510. 1.56e-111
 5     5 BraA…            4.47         -0.399     7.29  494. 6.31e-108
 6     6 BraA…            2.65         -0.139     7.53  491. 1.88e-107
 7     7 BraA…            2.11          0.281     6.87  477. 2.91e-104
 8     8 BraA…            3.09         -0.124     5.97  471. 5.85e-103
 9     9 BraA…            3.07          0.179     7.57  470. 7.61e-103
10    10 BraA…            2.45          0.0962    4.91  467. 3.40e-102
# ... with 14,064 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$leaf.densityun_densityun.trtlive.DEGs.int.rD.rCR.v3.0anno
# A tibble: 14,074 x 12
      X1 genes logFC.densityun logFC.densityun… logCPM    LR    PValue
   <int> <chr>           <dbl>            <dbl>  <dbl> <dbl>     <dbl>
 1     1 BraA…            6.65          1.09      4.09  891. 2.88e-194
 2     2 BraA…            2.63          0.0205    8.15  664. 7.63e-145
 3     3 BraA…            2.67         -0.00762   7.37  574. 1.78e-125
 4     4 BraA…           -4.25          0.267     7.24  510. 1.56e-111
 5     5 BraA…            4.07          0.399     7.29  494. 6.31e-108
 6     6 BraA…            2.51          0.139     7.53  491. 1.88e-107
 7     7 BraA…            2.39         -0.281     6.87  477. 2.91e-104
 8     8 BraA…            2.97          0.124     5.97  471. 5.85e-103
 9     9 BraA…            3.25         -0.179     7.57  470. 7.61e-103
10    10 BraA…            2.55         -0.0962    4.91  467. 3.40e-102
# ... with 14,064 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$leaf.densityun.DEGs.add.rD.rCR.v3.0anno
# A tibble: 14,919 x 11
      X1 genes logFC logCPM    LR    PValue       FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>     <dbl>     <dbl> <chr> <chr>    
 1     1 BraA…  7.03   4.09  860. 5.16e-189 1.23e-184 AT1G… ARR4     
 2     2 BraA…  2.64   8.15  678. 1.81e-149 2.16e-145 AT5G… RPL4     
 3     3 BraA…  2.67   7.37  588. 6.29e-130 5.01e-126 AT1G… ARP1     
 4     4 BraA… -4.11   7.24  512. 2.09e-113 1.25e-109 AT5G… <NA>     
 5     5 BraA…  2.58   7.53  497. 3.90e-110 1.86e-106 AT4G… HLN      
 6     6 BraA…  4.26   7.29  485. 1.51e-107 6.00e-104 AT5G… ATHD2    
 7     7 BraA…  3.03   5.97  480. 1.91e-106 6.52e-103 AT3G… <NA>     
 8     8 BraA…  2.50   4.91  478. 6.82e-106 2.04e-102 AT2G… ASHR2    
 9     9 BraA…  3.16   7.57  475. 2.11e-105 5.60e-102 AT5G… ATHD2    
10    10 BraA…  2.25   6.87  460. 5.80e-102 1.39e- 98 AT5G… NAP1;3   
# ... with 14,909 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$leaf.densityun.DEGs.add.rL.rCR.v3.0anno
# A tibble: 14,919 x 11
      X1 genes logFC logCPM    LR    PValue       FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>     <dbl>     <dbl> <chr> <chr>    
 1     1 BraA…  7.03   4.09  860. 5.16e-189 1.23e-184 AT1G… ARR4     
 2     2 BraA…  2.64   8.15  678. 1.81e-149 2.16e-145 AT5G… RPL4     
 3     3 BraA…  2.67   7.37  588. 6.29e-130 5.01e-126 AT1G… ARP1     
 4     4 BraA… -4.11   7.24  512. 2.09e-113 1.25e-109 AT5G… <NA>     
 5     5 BraA…  2.58   7.53  497. 3.90e-110 1.86e-106 AT4G… HLN      
 6     6 BraA…  4.26   7.29  485. 1.51e-107 6.00e-104 AT5G… ATHD2    
 7     7 BraA…  3.03   5.97  480. 1.91e-106 6.52e-103 AT3G… <NA>     
 8     8 BraA…  2.50   4.91  478. 6.82e-106 2.04e-102 AT2G… ASHR2    
 9     9 BraA…  3.16   7.57  475. 2.11e-105 5.60e-102 AT5G… ATHD2    
10    10 BraA…  2.25   6.87  460. 5.80e-102 1.39e- 98 AT5G… NAP1;3   
# ... with 14,909 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$leaf.densityun.trtdead.DEGs.int.rL.rCR.v3.0anno
# A tibble: 2 x 12
     X1 genes logFC logCPM    LR  PValue    FDR  X1_1 AGI   At_symbol
  <int> <chr> <dbl>  <dbl> <dbl>   <dbl>  <dbl> <int> <chr> <chr>    
1     1 BraA…  2.00  4.58   22.9 1.69e-6 0.0271 23774 AT1G… ARR7     
2     2 BraA…  3.95  0.659  22.3 2.27e-6 0.0271 33024 AT1G… <NA>     
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>

$leaf.densityun.trtlive.DEGs.int.rD.rCR.v3.0anno
# A tibble: 2 x 11
     X1 genes logFC logCPM    LR  PValue    FDR AGI   At_symbol
  <int> <chr> <dbl>  <dbl> <dbl>   <dbl>  <dbl> <chr> <chr>    
1     1 BraA… -2.00  4.58   22.9 1.69e-6 0.0271 AT1G… ARR7     
2     2 BraA… -3.95  0.659  22.3 2.27e-6 0.0271 AT1G… <NA>     
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>

$leaf.trtdead_densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno
# A tibble: 63 x 12
      X1 genes logFC.trtdead logFC.densitycr… logCPM    LR  PValue     FDR
   <int> <chr>         <dbl>            <dbl>  <dbl> <dbl>   <dbl>   <dbl>
 1     1 BraA…       -0.276            -0.766  7.58   29.4 4.09e-7 0.00976
 2     2 BraA…       -0.489            -0.376  4.13   26.8 1.54e-6 0.0177 
 3     3 BraA…        0.758             2.15   0.654  25.6 2.74e-6 0.0177 
 4     4 BraA…        0.189             0.714  4.94   25.2 3.36e-6 0.0177 
 5     5 BraA…       -0.0786           -1.22   5.52   24.7 4.23e-6 0.0177 
 6     6 BraA…        0.192             0.772  4.89   24.6 4.45e-6 0.0177 
 7     7 BraA…        0.124             1.14   4.46   24.1 5.93e-6 0.0186 
 8     8 BraA…        1.25             -3.95   0.659  23.9 6.59e-6 0.0186 
 9     9 BraA…        0.0242           -1.70   3.11   23.5 7.77e-6 0.0186 
10    10 BraA…        0.916            -2.00   4.58   23.5 7.80e-6 0.0186 
# ... with 53 more rows, and 4 more variables: AGI <chr>, At_symbol <chr>,
#   At_short_description <chr>, perc_ID <dbl>

$leaf.trtdead_densityun.trtdead.DEGs.int.rL.rCR.v3.0anno
# A tibble: 63 x 12
      X1 genes logFC.trtdead logFC.densityun… logCPM    LR  PValue     FDR
   <int> <chr>         <dbl>            <dbl>  <dbl> <dbl>   <dbl>   <dbl>
 1     1 BraA…        -1.04             0.766  7.58   29.4 4.09e-7 0.00976
 2     2 BraA…        -0.865            0.376  4.13   26.8 1.54e-6 0.0177 
 3     3 BraA…         2.90            -2.15   0.654  25.6 2.74e-6 0.0177 
 4     4 BraA…         0.903           -0.714  4.94   25.2 3.36e-6 0.0177 
 5     5 BraA…        -1.30             1.22   5.52   24.7 4.23e-6 0.0177 
 6     6 BraA…         0.964           -0.772  4.89   24.6 4.45e-6 0.0177 
 7     7 BraA…         1.27            -1.14   4.46   24.1 5.93e-6 0.0186 
 8     8 BraA…        -2.70             3.95   0.659  23.9 6.59e-6 0.0186 
 9     9 BraA…        -1.67             1.70   3.11   23.5 7.77e-6 0.0186 
10    10 BraA…        -1.09             2.00   4.58   23.5 7.80e-6 0.0186 
# ... with 53 more rows, and 4 more variables: AGI <chr>, At_symbol <chr>,
#   At_short_description <chr>, perc_ID <dbl>

$leaf.trtdead.DEGs.add.rL.rCR.v3.0anno
# A tibble: 3 x 11
     X1 genes  logFC logCPM    LR  PValue    FDR AGI   At_symbol
  <int> <chr>  <dbl>  <dbl> <dbl>   <dbl>  <dbl> <chr> <chr>    
1     1 BraA… -0.702  4.13   24.5 7.56e-7 0.0181 AT5G… <NA>     
2     2 BraA… -0.599  5.50   21.2 4.08e-6 0.0375 AT5G… ORP3C    
3     3 BraA… -1.92   0.414  21.0 4.71e-6 0.0375 AT5G… <NA>     
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>

$leaf.trtdead.DEGs.add.rL.rUN.v3.0anno
# A tibble: 3 x 11
     X1 genes  logFC logCPM    LR  PValue    FDR AGI   At_symbol
  <int> <chr>  <dbl>  <dbl> <dbl>   <dbl>  <dbl> <chr> <chr>    
1     1 BraA… -0.702  4.13   24.5 7.56e-7 0.0181 AT5G… <NA>     
2     2 BraA… -0.599  5.50   21.2 4.08e-6 0.0375 AT5G… ORP3C    
3     3 BraA… -1.92   0.414  21.0 4.71e-6 0.0375 AT5G… <NA>     
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>

$leaf.trtdead.DEGs.int.rL.rCR.v3.0anno
# A tibble: 370 x 11
      X1 genes  logFC logCPM    LR  PValue     FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>   <dbl>   <dbl> <chr> <chr>    
 1     1 BraA… -1.04   7.58   27.5 1.57e-7 0.00374 AT5G… AtHsp90-3
 2     2 BraA… -1.30   5.52   24.7 6.80e-7 0.00491 AT2G… <NA>     
 3     3 BraA…  1.27   4.46   23.8 1.06e-6 0.00491 AT1G… HHO6     
 4     4 BraA…  0.903  4.94   23.8 1.07e-6 0.00491 AT4G… PDE327   
 5     5 BraA…  0.964  4.89   23.6 1.19e-6 0.00491 AT5G… ATFTSZ1-1
 6     6 BraA… -1.67   3.11   23.5 1.23e-6 0.00491 AT5G… <NA>     
 7     7 BraA…  0.856  4.77   22.5 2.13e-6 0.00727 AT4G… ATCAD7   
 8     8 BraA…  2.90   0.654  21.7 3.20e-6 0.00857 AT4G… AtGGCT2;2
 9     9 BraA…  0.938  7.04   21.6 3.29e-6 0.00857 AT1G… AtPMT3   
10    10 BraA… -0.865  4.13   21.5 3.59e-6 0.00857 AT5G… <NA>     
# ... with 360 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$leaf.trtdead.DEGs.int.rL.rUN.v3.0anno
# A tibble: 0 x 11
# ... with 11 variables: X1 <int>, genes <chr>, logFC <dbl>, logCPM <dbl>,
#   LR <dbl>, PValue <dbl>, FDR <dbl>, AGI <chr>, At_symbol <chr>,
#   At_short_description <chr>, perc_ID <dbl>

$leaf.trtlive_densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno
# A tibble: 63 x 12
      X1 genes logFC.trtlive logFC.densitycr… logCPM    LR  PValue     FDR
   <int> <chr>         <dbl>            <dbl>  <dbl> <dbl>   <dbl>   <dbl>
 1     1 BraA…        0.276             0.766  7.58   29.4 4.09e-7 0.00976
 2     2 BraA…        0.489             0.376  4.13   26.8 1.54e-6 0.0177 
 3     3 BraA…       -0.758            -2.15   0.654  25.6 2.74e-6 0.0177 
 4     4 BraA…       -0.189            -0.714  4.94   25.2 3.36e-6 0.0177 
 5     5 BraA…        0.0786            1.22   5.52   24.7 4.23e-6 0.0177 
 6     6 BraA…       -0.192            -0.772  4.89   24.6 4.45e-6 0.0177 
 7     7 BraA…       -0.124            -1.14   4.46   24.1 5.93e-6 0.0186 
 8     8 BraA…       -1.25              3.95   0.659  23.9 6.59e-6 0.0186 
 9     9 BraA…       -0.0242            1.70   3.11   23.5 7.77e-6 0.0186 
10    10 BraA…       -0.916             2.00   4.58   23.5 7.80e-6 0.0186 
# ... with 53 more rows, and 4 more variables: AGI <chr>, At_symbol <chr>,
#   At_short_description <chr>, perc_ID <dbl>

$leaf.trtlive_densityun.trtlive.DEGs.int.rD.rCR.v3.0anno
# A tibble: 63 x 12
      X1 genes logFC.trtlive logFC.densityun… logCPM    LR  PValue     FDR
   <int> <chr>         <dbl>            <dbl>  <dbl> <dbl>   <dbl>   <dbl>
 1     1 BraA…         1.04            -0.766  7.58   29.4 4.09e-7 0.00976
 2     2 BraA…         0.865           -0.376  4.13   26.8 1.54e-6 0.0177 
 3     3 BraA…        -2.90             2.15   0.654  25.6 2.74e-6 0.0177 
 4     4 BraA…        -0.903            0.714  4.94   25.2 3.36e-6 0.0177 
 5     5 BraA…         1.30            -1.22   5.52   24.7 4.23e-6 0.0177 
 6     6 BraA…        -0.964            0.772  4.89   24.6 4.45e-6 0.0177 
 7     7 BraA…        -1.27             1.14   4.46   24.1 5.93e-6 0.0186 
 8     8 BraA…         2.70            -3.95   0.659  23.9 6.59e-6 0.0186 
 9     9 BraA…         1.67            -1.70   3.11   23.5 7.77e-6 0.0186 
10    10 BraA…         1.09            -2.00   4.58   23.5 7.80e-6 0.0186 
# ... with 53 more rows, and 4 more variables: AGI <chr>, At_symbol <chr>,
#   At_short_description <chr>, perc_ID <dbl>

$leaf.trtlive.DEGs.add.rD.rCR.v3.0anno
# A tibble: 3 x 11
     X1 genes logFC logCPM    LR  PValue    FDR AGI   At_symbol
  <int> <chr> <dbl>  <dbl> <dbl>   <dbl>  <dbl> <chr> <chr>    
1     1 BraA… 0.702  4.13   24.5 7.56e-7 0.0181 AT5G… <NA>     
2     2 BraA… 0.599  5.50   21.2 4.08e-6 0.0375 AT5G… ORP3C    
3     3 BraA… 1.92   0.414  21.0 4.71e-6 0.0375 AT5G… <NA>     
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>

$leaf.trtlive.DEGs.add.rD.rUN.v3.0anno
# A tibble: 3 x 11
     X1 genes logFC logCPM    LR  PValue    FDR AGI   At_symbol
  <int> <chr> <dbl>  <dbl> <dbl>   <dbl>  <dbl> <chr> <chr>    
1     1 BraA… 0.702  4.13   24.5 7.56e-7 0.0181 AT5G… <NA>     
2     2 BraA… 0.599  5.50   21.2 4.08e-6 0.0375 AT5G… ORP3C    
3     3 BraA… 1.92   0.414  21.0 4.71e-6 0.0375 AT5G… <NA>     
# ... with 2 more variables: At_short_description <chr>, perc_ID <dbl>

$leaf.trtlive.DEGs.int.rD.rCR.v3.0anno
# A tibble: 370 x 11
      X1 genes  logFC logCPM    LR  PValue     FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>   <dbl>   <dbl> <chr> <chr>    
 1     1 BraA…  1.04   7.58   27.5 1.57e-7 0.00374 AT5G… AtHsp90-3
 2     2 BraA…  1.30   5.52   24.7 6.80e-7 0.00491 AT2G… <NA>     
 3     3 BraA… -1.27   4.46   23.8 1.06e-6 0.00491 AT1G… HHO6     
 4     4 BraA… -0.903  4.94   23.8 1.07e-6 0.00491 AT4G… PDE327   
 5     5 BraA… -0.964  4.89   23.6 1.19e-6 0.00491 AT5G… ATFTSZ1-1
 6     6 BraA…  1.67   3.11   23.5 1.23e-6 0.00491 AT5G… <NA>     
 7     7 BraA… -0.856  4.77   22.5 2.13e-6 0.00727 AT4G… ATCAD7   
 8     8 BraA… -2.90   0.654  21.7 3.20e-6 0.00857 AT4G… AtGGCT2;2
 9     9 BraA… -0.938  7.04   21.6 3.29e-6 0.00857 AT1G… AtPMT3   
10    10 BraA…  0.865  4.13   21.5 3.59e-6 0.00857 AT5G… <NA>     
# ... with 360 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$leaf.trtlive.DEGs.int.rD.rUN.v3.0anno
# A tibble: 0 x 11
# ... with 11 variables: X1 <int>, genes <chr>, logFC <dbl>, logCPM <dbl>,
#   LR <dbl>, PValue <dbl>, FDR <dbl>, AGI <chr>, At_symbol <chr>,
#   At_short_description <chr>, perc_ID <dbl>

$leaf.un.trtlive.DEGs.all.rD.v3.0anno
# A tibble: 0 x 11
# ... with 11 variables: X1 <int>, genes <chr>, logFC <dbl>, logCPM <dbl>,
#   LR <dbl>, PValue <dbl>, FDR <dbl>, AGI <chr>, At_symbol <chr>,
#   At_short_description <chr>, perc_ID <dbl>

$root.cr.trtlive.DEGs.all.rD.v3.0anno
# A tibble: 3,887 x 11
      X1 genes  logFC logCPM    LR   PValue      FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>    <dbl>    <dbl> <chr> <chr>    
 1     1 BraA… -1.96    4.70  87.7 7.54e-21 1.07e-16 AT1G… ASP4     
 2     2 BraA…  1.22    5.63  87.6 8.17e-21 1.07e-16 AT2G… <NA>     
 3     3 BraA…  1.28    5.28  83.6 6.07e-20 5.29e-16 AT1G… BRR2     
 4     4 BraA… -1.15    5.99  81.6 1.70e-19 1.11e-15 AT2G… <NA>     
 5     5 BraA…  1.14    7.09  75.2 4.17e-18 2.18e-14 AT1G… BRR2     
 6     6 BraA…  1.02    5.44  74.1 7.24e-18 3.16e-14 AT5G… <NA>     
 7     7 BraA…  1.94    3.77  71.4 2.91e-17 1.09e-13 AT3G… TIC      
 8     8 BraA…  0.928   7.49  69.8 6.47e-17 2.03e-13 AT2G… ATGSL03  
 9     9 BraA…  1.59    3.73  69.7 6.98e-17 2.03e-13 AT1G… ASU1     
10    10 BraA…  1.30    3.72  66.9 2.79e-16 7.10e-13 AT5G… <NA>     
# ... with 3,877 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.densitycr_densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno
# A tibble: 8,708 x 12
      X1 genes logFC.densitycr logFC.densitycr… logCPM    LR    PValue
   <int> <chr>           <dbl>            <dbl>  <dbl> <dbl>     <dbl>
 1     1 BraA…           -2.88           0.498    5.32  778. 1.17e-169
 2     2 BraA…            2.50          -0.287    4.42  511. 1.05e-111
 3     3 BraA…           -3.53           1.22     6.17  491. 2.16e-107
 4     4 BraA…           -3.95           1.12     4.01  486. 2.51e-106
 5     5 BraA…           -4.44          -0.0881   4.23  454. 2.05e- 99
 6     6 BraA…           -2.58           0.467    6.28  445. 2.56e- 97
 7     7 BraA…            2.08          -0.172    7.33  441. 2.06e- 96
 8     8 BraA…            3.07           0.696    4.36  421. 4.47e- 92
 9     9 BraA…           -3.22           0.782    5.90  383. 5.42e- 84
10    10 BraA…           -2.31           0.691    4.98  375. 3.95e- 82
# ... with 8,698 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$root.densitycr_densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno
# A tibble: 8,708 x 12
      X1 genes logFC.densitycr logFC.densitycr… logCPM    LR    PValue
   <int> <chr>           <dbl>            <dbl>  <dbl> <dbl>     <dbl>
 1     1 BraA…           -2.38          -0.498    5.32  778. 1.17e-169
 2     2 BraA…            2.21           0.287    4.42  511. 1.05e-111
 3     3 BraA…           -2.31          -1.22     6.17  491. 2.16e-107
 4     4 BraA…           -2.83          -1.12     4.01  486. 2.51e-106
 5     5 BraA…           -4.53           0.0881   4.23  454. 2.05e- 99
 6     6 BraA…           -2.11          -0.467    6.28  445. 2.56e- 97
 7     7 BraA…            1.90           0.172    7.33  441. 2.06e- 96
 8     8 BraA…            3.76          -0.696    4.36  421. 4.47e- 92
 9     9 BraA…           -2.44          -0.782    5.90  383. 5.42e- 84
10    10 BraA…           -1.62          -0.691    4.98  375. 3.95e- 82
# ... with 8,698 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$root.densitycr.DEGs.add.rD.rUN.v3.0anno
# A tibble: 8,363 x 11
      X1 genes logFC logCPM    LR    PValue       FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>     <dbl>     <dbl> <chr> <chr>    
 1     1 BraA… -2.62   5.32  656. 1.22e-144 3.21e-140 AT1G… AST56    
 2     2 BraA…  2.36   4.42  494. 1.97e-109 2.60e-105 AT1G… NLP4     
 3     3 BraA… -4.48   4.23  458. 1.38e-101 1.22e- 97 AT3G… ATIPT3   
 4     4 BraA…  1.99   7.33  436. 9.96e- 97 6.56e- 93 AT5G… AAP2     
 5     5 BraA… -2.34   6.28  395. 6.92e- 88 3.65e- 84 AT1G… ATTPPB   
 6     6 BraA…  3.38   4.35  370. 2.32e- 82 1.02e- 78 AT5G… <NA>     
 7     7 BraA…  6.68   3.06  368. 5.13e- 82 1.93e- 78 AT3G… NLP9     
 8     8 BraA… -2.47   5.28  358. 9.38e- 80 3.09e- 76 AT1G… ATATP-PR…
 9     9 BraA…  2.81   4.13  342. 1.82e- 76 5.33e- 73 AT5G… <NA>     
10    10 BraA… -3.34   4.01  336. 4.16e- 75 1.04e- 71 AT5G… <NA>     
# ... with 8,353 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.densitycr.DEGs.add.rL.rUN.v3.0anno
# A tibble: 8,363 x 11
      X1 genes logFC logCPM    LR    PValue       FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>     <dbl>     <dbl> <chr> <chr>    
 1     1 BraA… -2.62   5.32  656. 1.22e-144 3.21e-140 AT1G… AST56    
 2     2 BraA…  2.36   4.42  494. 1.97e-109 2.60e-105 AT1G… NLP4     
 3     3 BraA… -4.48   4.23  458. 1.38e-101 1.22e- 97 AT3G… ATIPT3   
 4     4 BraA…  1.99   7.33  436. 9.96e- 97 6.56e- 93 AT5G… AAP2     
 5     5 BraA… -2.34   6.28  395. 6.92e- 88 3.65e- 84 AT1G… ATTPPB   
 6     6 BraA…  3.38   4.35  370. 2.32e- 82 1.02e- 78 AT5G… <NA>     
 7     7 BraA…  6.68   3.06  368. 5.13e- 82 1.93e- 78 AT3G… NLP9     
 8     8 BraA… -2.47   5.28  358. 9.38e- 80 3.09e- 76 AT1G… ATATP-PR…
 9     9 BraA…  2.81   4.13  342. 1.82e- 76 5.33e- 73 AT5G… <NA>     
10    10 BraA… -3.34   4.01  336. 4.16e- 75 1.04e- 71 AT5G… <NA>     
# ... with 8,353 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno
# A tibble: 471 x 11
      X1 genes logFC logCPM    LR   PValue     FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>    <dbl>   <dbl> <chr> <chr>    
 1     1 BraA…  2.06  4.03   41.3 1.28e-10 3.36e-6 AT3G… BHLH039  
 2     2 BraA…  1.60  5.88   36.8 1.33e- 9 1.75e-5 AT1G… ASP4     
 3     3 BraA…  1.11  6.78   32.4 1.27e- 8 1.12e-4 AT1G… ATSBT5.2 
 4     4 BraA…  3.40  5.12   28.1 1.13e- 7 7.45e-4 AT3G… <NA>     
 5     5 BraA…  1.50  4.22   26.7 2.33e- 7 1.14e-3 AT4G… ATIRT1   
 6     6 BraA…  3.19  2.39   26.5 2.60e- 7 1.14e-3 AT1G… GAT      
 7     7 BraA…  3.72  0.831  24.9 6.10e- 7 2.10e-3 AT5G… <NA>     
 8     8 BraA…  1.72  5.26   24.8 6.39e- 7 2.10e-3 AT5G… AtCOMT   
 9     9 BraA…  2.14  5.04   24.0 9.43e- 7 2.76e-3 AT3G… F6'H1    
10    10 BraA…  1.84  4.05   23.8 1.08e- 6 2.84e-3 AT4G… <NA>     
# ... with 461 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno
# A tibble: 471 x 11
      X1 genes logFC logCPM    LR   PValue     FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>    <dbl>   <dbl> <chr> <chr>    
 1     1 BraA… -2.06  4.03   41.3 1.28e-10 3.36e-6 AT3G… BHLH039  
 2     2 BraA… -1.60  5.88   36.8 1.33e- 9 1.75e-5 AT1G… ASP4     
 3     3 BraA… -1.11  6.78   32.4 1.27e- 8 1.12e-4 AT1G… ATSBT5.2 
 4     4 BraA… -3.40  5.12   28.1 1.13e- 7 7.45e-4 AT3G… <NA>     
 5     5 BraA… -1.50  4.22   26.7 2.33e- 7 1.14e-3 AT4G… ATIRT1   
 6     6 BraA… -3.19  2.39   26.5 2.60e- 7 1.14e-3 AT1G… GAT      
 7     7 BraA… -3.72  0.831  24.9 6.10e- 7 2.10e-3 AT5G… <NA>     
 8     8 BraA… -1.72  5.26   24.8 6.39e- 7 2.10e-3 AT5G… AtCOMT   
 9     9 BraA… -2.14  5.04   24.0 9.43e- 7 2.76e-3 AT3G… F6'H1    
10    10 BraA… -1.84  4.05   23.8 1.08e- 6 2.84e-3 AT4G… <NA>     
# ... with 461 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.densityun_densityun.trtdead.DEGs.int.rL.rCR.v3.0anno
# A tibble: 8,708 x 12
      X1 genes logFC.densityun logFC.densityun… logCPM    LR    PValue
   <int> <chr>           <dbl>            <dbl>  <dbl> <dbl>     <dbl>
 1     1 BraA…            2.88          -0.498    5.32  778. 1.17e-169
 2     2 BraA…           -2.50           0.287    4.42  511. 1.05e-111
 3     3 BraA…            3.53          -1.22     6.17  491. 2.16e-107
 4     4 BraA…            3.95          -1.12     4.01  486. 2.51e-106
 5     5 BraA…            4.44           0.0881   4.23  454. 2.05e- 99
 6     6 BraA…            2.58          -0.467    6.28  445. 2.56e- 97
 7     7 BraA…           -2.08           0.172    7.33  441. 2.06e- 96
 8     8 BraA…           -3.07          -0.696    4.36  421. 4.47e- 92
 9     9 BraA…            3.22          -0.782    5.90  383. 5.42e- 84
10    10 BraA…            2.31          -0.691    4.98  375. 3.95e- 82
# ... with 8,698 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$root.densityun_densityun.trtlive.DEGs.int.rD.rCR.v3.0anno
# A tibble: 8,708 x 12
      X1 genes logFC.densityun logFC.densityun… logCPM    LR    PValue
   <int> <chr>           <dbl>            <dbl>  <dbl> <dbl>     <dbl>
 1     1 BraA…            2.38           0.498    5.32  778. 1.17e-169
 2     2 BraA…           -2.21          -0.287    4.42  511. 1.05e-111
 3     3 BraA…            2.31           1.22     6.17  491. 2.16e-107
 4     4 BraA…            2.83           1.12     4.01  486. 2.51e-106
 5     5 BraA…            4.53          -0.0881   4.23  454. 2.05e- 99
 6     6 BraA…            2.11           0.467    6.28  445. 2.56e- 97
 7     7 BraA…           -1.90          -0.172    7.33  441. 2.06e- 96
 8     8 BraA…           -3.76           0.696    4.36  421. 4.47e- 92
 9     9 BraA…            2.44           0.782    5.90  383. 5.42e- 84
10    10 BraA…            1.62           0.691    4.98  375. 3.95e- 82
# ... with 8,698 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$root.densityun.DEGs.add.rD.rCR.v3.0anno
# A tibble: 8,363 x 11
      X1 genes logFC logCPM    LR    PValue       FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>     <dbl>     <dbl> <chr> <chr>    
 1     1 BraA…  2.62   5.32  656. 1.22e-144 3.21e-140 AT1G… AST56    
 2     2 BraA… -2.36   4.42  494. 1.97e-109 2.60e-105 AT1G… NLP4     
 3     3 BraA…  4.48   4.23  458. 1.38e-101 1.22e- 97 AT3G… ATIPT3   
 4     4 BraA… -1.99   7.33  436. 9.96e- 97 6.56e- 93 AT5G… AAP2     
 5     5 BraA…  2.34   6.28  395. 6.92e- 88 3.65e- 84 AT1G… ATTPPB   
 6     6 BraA… -3.38   4.35  370. 2.32e- 82 1.02e- 78 AT5G… <NA>     
 7     7 BraA… -6.68   3.06  368. 5.13e- 82 1.93e- 78 AT3G… NLP9     
 8     8 BraA…  2.47   5.28  358. 9.38e- 80 3.09e- 76 AT1G… ATATP-PR…
 9     9 BraA… -2.81   4.13  342. 1.82e- 76 5.33e- 73 AT5G… <NA>     
10    10 BraA…  3.34   4.01  336. 4.16e- 75 1.04e- 71 AT5G… <NA>     
# ... with 8,353 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.densityun.DEGs.add.rL.rCR.v3.0anno
# A tibble: 8,363 x 11
      X1 genes logFC logCPM    LR    PValue       FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>     <dbl>     <dbl> <chr> <chr>    
 1     1 BraA…  2.62   5.32  656. 1.22e-144 3.21e-140 AT1G… AST56    
 2     2 BraA… -2.36   4.42  494. 1.97e-109 2.60e-105 AT1G… NLP4     
 3     3 BraA…  4.48   4.23  458. 1.38e-101 1.22e- 97 AT3G… ATIPT3   
 4     4 BraA… -1.99   7.33  436. 9.96e- 97 6.56e- 93 AT5G… AAP2     
 5     5 BraA…  2.34   6.28  395. 6.92e- 88 3.65e- 84 AT1G… ATTPPB   
 6     6 BraA… -3.38   4.35  370. 2.32e- 82 1.02e- 78 AT5G… <NA>     
 7     7 BraA… -6.68   3.06  368. 5.13e- 82 1.93e- 78 AT3G… NLP9     
 8     8 BraA…  2.47   5.28  358. 9.38e- 80 3.09e- 76 AT1G… ATATP-PR…
 9     9 BraA… -2.81   4.13  342. 1.82e- 76 5.33e- 73 AT5G… <NA>     
10    10 BraA…  3.34   4.01  336. 4.16e- 75 1.04e- 71 AT5G… <NA>     
# ... with 8,353 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.densityun.trtdead.DEGs.int.rL.rCR.v3.0anno
# A tibble: 471 x 12
      X1 genes logFC logCPM    LR   PValue     FDR  X1_1 AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>    <dbl>   <dbl> <int> <chr> <chr>    
 1     1 BraA… -2.06  4.03   41.3 1.28e-10 3.36e-6 15390 AT3G… BHLH039  
 2     2 BraA… -1.60  5.88   36.8 1.33e- 9 1.75e-5 35547 AT1G… ASP4     
 3     3 BraA… -1.11  6.78   32.4 1.27e- 8 1.12e-4 23863 AT1G… ATSBT5.2 
 4     4 BraA… -3.40  5.12   28.1 1.13e- 7 7.45e-4  4032 AT3G… <NA>     
 5     5 BraA… -1.50  4.22   26.7 2.33e- 7 1.14e-3  1149 AT4G… ATIRT1   
 6     6 BraA… -3.19  2.39   26.5 2.60e- 7 1.14e-3 39482 AT1G… GAT      
 7     7 BraA… -3.72  0.831  24.9 6.10e- 7 2.10e-3 28198 AT5G… <NA>     
 8     8 BraA… -1.72  5.26   24.8 6.39e- 7 2.10e-3 14171 AT5G… AtCOMT   
 9     9 BraA… -2.14  5.04   24.0 9.43e- 7 2.76e-3 21279 AT3G… F6'H1    
10    10 BraA… -1.84  4.05   23.8 1.08e- 6 2.84e-3   771 AT4G… <NA>     
# ... with 461 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.densityun.trtlive.DEGs.int.rD.rCR.v3.0anno
# A tibble: 471 x 11
      X1 genes logFC logCPM    LR   PValue     FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>    <dbl>   <dbl> <chr> <chr>    
 1     1 BraA…  2.06  4.03   41.3 1.28e-10 3.36e-6 AT3G… BHLH039  
 2     2 BraA…  1.60  5.88   36.8 1.33e- 9 1.75e-5 AT1G… ASP4     
 3     3 BraA…  1.11  6.78   32.4 1.27e- 8 1.12e-4 AT1G… ATSBT5.2 
 4     4 BraA…  3.40  5.12   28.1 1.13e- 7 7.45e-4 AT3G… <NA>     
 5     5 BraA…  1.50  4.22   26.7 2.33e- 7 1.14e-3 AT4G… ATIRT1   
 6     6 BraA…  3.19  2.39   26.5 2.60e- 7 1.14e-3 AT1G… GAT      
 7     7 BraA…  3.72  0.831  24.9 6.10e- 7 2.10e-3 AT5G… <NA>     
 8     8 BraA…  1.72  5.26   24.8 6.39e- 7 2.10e-3 AT5G… AtCOMT   
 9     9 BraA…  2.14  5.04   24.0 9.43e- 7 2.76e-3 AT3G… F6'H1    
10    10 BraA…  1.84  4.05   23.8 1.08e- 6 2.84e-3 AT4G… <NA>     
# ... with 461 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.trtdead_densitycr.trtdead.DEGs.int.rL.rUN.v3.0anno
# A tibble: 3,857 x 12
      X1 genes logFC.trtdead logFC.densitycr… logCPM    LR   PValue
   <int> <chr>         <dbl>            <dbl>  <dbl> <dbl>    <dbl>
 1     1 BraA…        0.370             1.60    5.88 105.  1.40e-23
 2     2 BraA…        0.0552            2.06    4.03  77.8 1.27e-17
 3     3 BraA…        0.372             0.682   6.91  73.4 1.16e-16
 4     4 BraA…        0.211             1.50    4.22  65.5 5.99e-15
 5     5 BraA…       -0.523            -0.132   8.54  63.6 1.56e-14
 6     6 BraA…       -0.331            -0.590   7.24  60.6 6.97e-14
 7     7 BraA…       -2.20              1.84    2.44  59.1 1.50e-13
 8     8 BraA…       -2.52              1.41    1.76  58.1 2.36e-13
 9     9 BraA…       -0.128            -0.895   5.25  56.8 4.62e-13
10    10 BraA…       -0.231            -0.989   5.48  55.3 9.90e-13
# ... with 3,847 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$root.trtdead_densityun.trtdead.DEGs.int.rL.rCR.v3.0anno
# A tibble: 3,857 x 12
      X1 genes logFC.trtdead logFC.densityun… logCPM    LR   PValue
   <int> <chr>         <dbl>            <dbl>  <dbl> <dbl>    <dbl>
 1     1 BraA…         1.97            -1.60    5.88 105.  1.40e-23
 2     2 BraA…         2.11            -2.06    4.03  77.8 1.27e-17
 3     3 BraA…         1.05            -0.682   6.91  73.4 1.16e-16
 4     4 BraA…         1.71            -1.50    4.22  65.5 5.99e-15
 5     5 BraA…        -0.655            0.132   8.54  63.6 1.56e-14
 6     6 BraA…        -0.921            0.590   7.24  60.6 6.97e-14
 7     7 BraA…        -0.353           -1.84    2.44  59.1 1.50e-13
 8     8 BraA…        -1.12            -1.41    1.76  58.1 2.36e-13
 9     9 BraA…        -1.02             0.895   5.25  56.8 4.62e-13
10    10 BraA…        -1.22             0.989   5.48  55.3 9.90e-13
# ... with 3,847 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$root.trtdead.DEGs.add.rL.rCR.v3.0anno
# A tibble: 3,352 x 11
      X1 genes  logFC logCPM    LR   PValue      FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>    <dbl>    <dbl> <chr> <chr>    
 1     1 BraA… -0.590   8.54  62.3 2.94e-15 7.74e-11 AT2G… ATUBC24  
 2     2 BraA…  2.18    1.59  55.7 8.55e-14 1.13e- 9 AT2G… <NA>     
 3     3 BraA…  1.10    2.65  49.2 2.27e-12 1.99e- 8 AT1G… <NA>     
 4     4 BraA…  0.482   6.84  46.0 1.17e-11 7.35e- 8 AT4G… <NA>     
 5     5 BraA… -1.61    1.61  45.3 1.67e-11 7.35e- 8 AT1G… IGMT2    
 6     6 BraA…  0.607   5.95  45.3 1.68e-11 7.35e- 8 AT2G… ATGSTU4  
 7     7 BraA… -0.528   6.88  44.9 2.07e-11 7.35e- 8 AT1G… ABCG35   
 8     8 BraA… -0.499   7.51  44.8 2.23e-11 7.35e- 8 AT1G… FB       
 9     9 BraA…  0.714   6.91  44.0 3.36e-11 9.82e- 8 AT1G… ATOPR2   
10    10 BraA… -0.569   6.15  43.5 4.27e-11 1.13e- 7 AT5G… CLPD     
# ... with 3,342 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.trtdead.DEGs.add.rL.rUN.v3.0anno
# A tibble: 3,352 x 11
      X1 genes  logFC logCPM    LR   PValue      FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>    <dbl>    <dbl> <chr> <chr>    
 1     1 BraA… -0.590   8.54  62.3 2.94e-15 7.74e-11 AT2G… ATUBC24  
 2     2 BraA…  2.18    1.59  55.7 8.55e-14 1.13e- 9 AT2G… <NA>     
 3     3 BraA…  1.10    2.65  49.2 2.27e-12 1.99e- 8 AT1G… <NA>     
 4     4 BraA…  0.482   6.84  46.0 1.17e-11 7.35e- 8 AT4G… <NA>     
 5     5 BraA… -1.61    1.61  45.3 1.67e-11 7.35e- 8 AT1G… IGMT2    
 6     6 BraA…  0.607   5.95  45.3 1.68e-11 7.35e- 8 AT2G… ATGSTU4  
 7     7 BraA… -0.528   6.88  44.9 2.07e-11 7.35e- 8 AT1G… ABCG35   
 8     8 BraA… -0.499   7.51  44.8 2.23e-11 7.35e- 8 AT1G… FB       
 9     9 BraA…  0.714   6.91  44.0 3.36e-11 9.82e- 8 AT1G… ATOPR2   
10    10 BraA… -0.569   6.15  43.5 4.27e-11 1.13e- 7 AT5G… CLPD     
# ... with 3,342 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.trtdead.DEGs.int.rL.rCR.v3.0anno
# A tibble: 3,434 x 11
      X1 genes  logFC logCPM    LR   PValue      FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>    <dbl>    <dbl> <chr> <chr>    
 1     1 BraA…  1.97    5.88 101.  9.26e-24 2.44e-19 AT1G… ASP4     
 2     2 BraA…  2.11    4.03  77.7 1.18e-18 1.55e-14 AT3G… BHLH039  
 3     3 BraA…  1.05    6.91  65.1 7.00e-16 6.15e-12 AT1G… ATOPR2   
 4     4 BraA…  1.71    4.22  64.3 1.05e-15 6.92e-12 AT4G… ATIRT1   
 5     5 BraA… -1.02    5.25  55.9 7.52e-14 3.96e-10 AT5G… <NA>     
 6     6 BraA… -0.921   7.24  53.6 2.47e-13 1.07e- 9 AT2G… ATGSL03  
 7     7 BraA… -1.22    5.48  53.3 2.83e-13 1.07e- 9 AT2G… <NA>     
 8     8 BraA…  1.81    5.26  51.7 6.49e-13 2.14e- 9 AT5G… AtCOMT   
 9     9 BraA…  1.16    5.96  50.9 9.52e-13 2.30e- 9 AT2G… <NA>     
10    10 BraA… -1.24    3.91  50.9 9.83e-13 2.30e- 9 AT4G… ATSPS4F  
# ... with 3,424 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.trtdead.DEGs.int.rL.rUN.v3.0anno
# A tibble: 357 x 11
      X1 genes  logFC logCPM    LR   PValue      FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>    <dbl>    <dbl> <chr> <chr>    
 1     1 BraA… -2.20   2.44   57.3 3.75e-14 9.87e-10 AT1G… ATGSTU12 
 2     2 BraA… -2.52   1.76   47.1 6.73e-12 7.82e- 8 AT2G… ATWRKY59 
 3     3 BraA… -4.03   0.831  46.6 8.91e-12 7.82e- 8 AT5G… <NA>     
 4     4 BraA… -1.40   3.53   41.0 1.52e-10 1.00e- 6 AT1G… HMS      
 5     5 BraA… -1.35   2.35   38.1 6.87e-10 3.27e- 6 AT2G… ANAC042  
 6     6 BraA… -2.08   3.27   37.9 7.45e-10 3.27e- 6 AT2G… <NA>     
 7     7 BraA… -1.97   5.83   34.1 5.13e- 9 1.93e- 5 AT4G… <NA>     
 8     8 BraA… -0.925  4.26   32.6 1.15e- 8 3.70e- 5 AT4G… CYP706A1 
 9     9 BraA… -1.86   2.87   32.4 1.26e- 8 3.70e- 5 AT2G… ANAC042  
10    10 BraA… -1.90   1.61   31.8 1.70e- 8 4.47e- 5 AT1G… IGMT2    
# ... with 347 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.trtlive_densitycr.trtlive.DEGs.int.rD.rUN.v3.0anno
# A tibble: 3,857 x 12
      X1 genes logFC.trtlive logFC.densitycr… logCPM    LR   PValue
   <int> <chr>         <dbl>            <dbl>  <dbl> <dbl>    <dbl>
 1     1 BraA…       -0.370            -1.60    5.88 105.  1.40e-23
 2     2 BraA…       -0.0552           -2.06    4.03  77.8 1.27e-17
 3     3 BraA…       -0.372            -0.682   6.91  73.4 1.16e-16
 4     4 BraA…       -0.211            -1.50    4.22  65.5 5.99e-15
 5     5 BraA…        0.523             0.132   8.54  63.6 1.56e-14
 6     6 BraA…        0.331             0.590   7.24  60.6 6.97e-14
 7     7 BraA…        2.20             -1.84    2.44  59.1 1.50e-13
 8     8 BraA…        2.52             -1.41    1.76  58.1 2.36e-13
 9     9 BraA…        0.128             0.895   5.25  56.8 4.62e-13
10    10 BraA…        0.231             0.989   5.48  55.3 9.90e-13
# ... with 3,847 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$root.trtlive_densityun.trtlive.DEGs.int.rD.rCR.v3.0anno
# A tibble: 3,857 x 12
      X1 genes logFC.trtlive logFC.densityun… logCPM    LR   PValue
   <int> <chr>         <dbl>            <dbl>  <dbl> <dbl>    <dbl>
 1     1 BraA…        -1.97             1.60    5.88 105.  1.40e-23
 2     2 BraA…        -2.11             2.06    4.03  77.8 1.27e-17
 3     3 BraA…        -1.05             0.682   6.91  73.4 1.16e-16
 4     4 BraA…        -1.71             1.50    4.22  65.5 5.99e-15
 5     5 BraA…         0.655           -0.132   8.54  63.6 1.56e-14
 6     6 BraA…         0.921           -0.590   7.24  60.6 6.97e-14
 7     7 BraA…         0.353            1.84    2.44  59.1 1.50e-13
 8     8 BraA…         1.12             1.41    1.76  58.1 2.36e-13
 9     9 BraA…         1.02            -0.895   5.25  56.8 4.62e-13
10    10 BraA…         1.22            -0.989   5.48  55.3 9.90e-13
# ... with 3,847 more rows, and 5 more variables: FDR <dbl>, AGI <chr>,
#   At_symbol <chr>, At_short_description <chr>, perc_ID <dbl>

$root.trtlive.DEGs.add.rD.rCR.v3.0anno
# A tibble: 3,352 x 11
      X1 genes  logFC logCPM    LR   PValue      FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>    <dbl>    <dbl> <chr> <chr>    
 1     1 BraA…  0.590   8.54  62.3 2.94e-15 7.74e-11 AT2G… ATUBC24  
 2     2 BraA… -2.18    1.59  55.7 8.55e-14 1.13e- 9 AT2G… <NA>     
 3     3 BraA… -1.10    2.65  49.2 2.27e-12 1.99e- 8 AT1G… <NA>     
 4     4 BraA… -0.482   6.84  46.0 1.17e-11 7.35e- 8 AT4G… <NA>     
 5     5 BraA…  1.61    1.61  45.3 1.67e-11 7.35e- 8 AT1G… IGMT2    
 6     6 BraA… -0.607   5.95  45.3 1.68e-11 7.35e- 8 AT2G… ATGSTU4  
 7     7 BraA…  0.528   6.88  44.9 2.07e-11 7.35e- 8 AT1G… ABCG35   
 8     8 BraA…  0.499   7.51  44.8 2.23e-11 7.35e- 8 AT1G… FB       
 9     9 BraA… -0.714   6.91  44.0 3.36e-11 9.82e- 8 AT1G… ATOPR2   
10    10 BraA…  0.569   6.15  43.5 4.27e-11 1.13e- 7 AT5G… CLPD     
# ... with 3,342 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.trtlive.DEGs.add.rD.rUN.v3.0anno
# A tibble: 3,352 x 11
      X1 genes  logFC logCPM    LR   PValue      FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>    <dbl>    <dbl> <chr> <chr>    
 1     1 BraA…  0.590   8.54  62.3 2.94e-15 7.74e-11 AT2G… ATUBC24  
 2     2 BraA… -2.18    1.59  55.7 8.55e-14 1.13e- 9 AT2G… <NA>     
 3     3 BraA… -1.10    2.65  49.2 2.27e-12 1.99e- 8 AT1G… <NA>     
 4     4 BraA… -0.482   6.84  46.0 1.17e-11 7.35e- 8 AT4G… <NA>     
 5     5 BraA…  1.61    1.61  45.3 1.67e-11 7.35e- 8 AT1G… IGMT2    
 6     6 BraA… -0.607   5.95  45.3 1.68e-11 7.35e- 8 AT2G… ATGSTU4  
 7     7 BraA…  0.528   6.88  44.9 2.07e-11 7.35e- 8 AT1G… ABCG35   
 8     8 BraA…  0.499   7.51  44.8 2.23e-11 7.35e- 8 AT1G… FB       
 9     9 BraA… -0.714   6.91  44.0 3.36e-11 9.82e- 8 AT1G… ATOPR2   
10    10 BraA…  0.569   6.15  43.5 4.27e-11 1.13e- 7 AT5G… CLPD     
# ... with 3,342 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.trtlive.DEGs.int.rD.rCR.v3.0anno
# A tibble: 3,434 x 11
      X1 genes  logFC logCPM    LR   PValue      FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>    <dbl>    <dbl> <chr> <chr>    
 1     1 BraA… -1.97    5.88 101.  9.26e-24 2.44e-19 AT1G… ASP4     
 2     2 BraA… -2.11    4.03  77.7 1.18e-18 1.55e-14 AT3G… BHLH039  
 3     3 BraA… -1.05    6.91  65.1 7.00e-16 6.15e-12 AT1G… ATOPR2   
 4     4 BraA… -1.71    4.22  64.3 1.05e-15 6.92e-12 AT4G… ATIRT1   
 5     5 BraA…  1.02    5.25  55.9 7.52e-14 3.96e-10 AT5G… <NA>     
 6     6 BraA…  0.921   7.24  53.6 2.47e-13 1.07e- 9 AT2G… ATGSL03  
 7     7 BraA…  1.22    5.48  53.3 2.83e-13 1.07e- 9 AT2G… <NA>     
 8     8 BraA… -1.81    5.26  51.7 6.49e-13 2.14e- 9 AT5G… AtCOMT   
 9     9 BraA… -1.16    5.96  50.9 9.52e-13 2.30e- 9 AT2G… <NA>     
10    10 BraA…  1.24    3.91  50.9 9.83e-13 2.30e- 9 AT4G… ATSPS4F  
# ... with 3,424 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.trtlive.DEGs.int.rD.rUN.v3.0anno
# A tibble: 357 x 11
      X1 genes logFC logCPM    LR   PValue      FDR AGI   At_symbol
   <int> <chr> <dbl>  <dbl> <dbl>    <dbl>    <dbl> <chr> <chr>    
 1     1 BraA… 2.20   2.44   57.3 3.75e-14 9.87e-10 AT1G… ATGSTU12 
 2     2 BraA… 2.52   1.76   47.1 6.73e-12 7.82e- 8 AT2G… ATWRKY59 
 3     3 BraA… 4.03   0.831  46.6 8.91e-12 7.82e- 8 AT5G… <NA>     
 4     4 BraA… 1.40   3.53   41.0 1.52e-10 1.00e- 6 AT1G… HMS      
 5     5 BraA… 1.35   2.35   38.1 6.87e-10 3.27e- 6 AT2G… ANAC042  
 6     6 BraA… 2.08   3.27   37.9 7.45e-10 3.27e- 6 AT2G… <NA>     
 7     7 BraA… 1.97   5.83   34.1 5.13e- 9 1.93e- 5 AT4G… <NA>     
 8     8 BraA… 0.925  4.26   32.6 1.15e- 8 3.70e- 5 AT4G… CYP706A1 
 9     9 BraA… 1.86   2.87   32.4 1.26e- 8 3.70e- 5 AT2G… ANAC042  
10    10 BraA… 1.90   1.61   31.8 1.70e- 8 4.47e- 5 AT1G… IGMT2    
# ... with 347 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>

$root.un.trtlive.DEGs.all.rD.v3.0anno
# A tibble: 297 x 11
      X1 genes  logFC logCPM    LR   PValue     FDR AGI   At_symbol
   <int> <chr>  <dbl>  <dbl> <dbl>    <dbl>   <dbl> <chr> <chr>    
 1     1 BraA…  2.19   2.37   56.7 5.00e-14 1.30e-9 AT1G… ATGSTU12 
 2     2 BraA…  2.06   3.30   47.4 5.87e-12 5.83e-8 AT2G… <NA>     
 3     3 BraA…  4.05   0.567  47.1 6.75e-12 5.83e-8 AT5G… <NA>     
 4     4 BraA…  2.52   1.68   46.1 1.13e-11 7.29e-8 AT2G… ATWRKY59 
 5     5 BraA… -2.17   1.80   45.7 1.41e-11 7.32e-8 AT2G… <NA>     
 6     6 BraA…  1.41   2.87   43.4 4.55e-11 1.97e-7 AT1G… HMS      
 7     7 BraA…  1.86   2.20   38.3 5.95e-10 2.20e-6 AT2G… ANAC042  
 8     8 BraA…  0.933  4.20   38.0 7.03e-10 2.28e-6 AT4G… CYP706A1 
 9     9 BraA…  1.46   1.59   37.5 9.38e-10 2.70e-6 AT5G… <NA>     
10    10 BraA…  1.90   1.67   36.6 1.48e- 9 3.84e-6 AT1G… IGMT2    
# ... with 287 more rows, and 2 more variables:
#   At_short_description <chr>, perc_ID <dbl>
DEG.count.list.e3.v3.0annotation.all.FDR0.05[["root.cr.trtlive.DEGs.all.rD.v3.0anno"]] %>% View() # OK. 3887 genes

# Expression pattern in exp1

# Expression pattern in exp3

# VennDiagram between exp1 FPsc root soil, exp3 cr root soil, exp3 un root soil.

---
title: "Expression_pattern_graph"
output: 
  flexdashboard::flex_dashboard:
    #css: libs/my-theme.css
    vertical_layout: scroll
    orientation: columns
    #social: menu
    source_code: embed
    #theme: default
editor_options: 
  chunk_output_type: console
---
```{r setup, include=FALSE}
library(knitr)
library(flexdashboard)
source("Expression_pattern_graph.R",chdir=TRUE) # reading necessary data from temporal workind directory where the file "Expression_Pattern_graph.R" locate.
#source("../../../tools/Expression_pattern_graph.R",chdir=TRUE)
# "/Volumes/data_work/Data8/NGS_related/Brassica_microbiome/Brapa_microbes/tools"
```

# Reading DEGs list exp1 {data-navmenu="Reading DEGs"}
===========================================
```{r echo=TRUE, message=FALSE, warning=FALSE, paged.print=FALSE, error=TRUE}
# all model including subset data
DEG.objs.e1.v3.0annotation.all<-list.files(path=file.path("..","v3.0annotation","20170617-samples","output","FULLtoptag"),
           pattern="(^leaf|^root)(\\.)(.+)(v3.0anno)(.csv)") 
# read csv file (only full model)
DEG.count.list.e1.v3.0annotation.all<-lapply(DEG.objs.e1.v3.0annotation.all, function(x) read_csv(paste(file.path("..","v3.0annotation","20170617-samples","output","FULLtoptag"),"/",x,sep="")))
names(DEG.count.list.e1.v3.0annotation.all)<-gsub(".csv","",DEG.objs.e1.v3.0annotation.all)
DEG.count.list.e1.v3.0annotation.all[["root.R500.trtlive.DEGs.all.rD.v3.0anno"]] %>% filter(FDR<0.05)
names(DEG.count.list.e1.v3.0annotation.all)
# FDR<0.05
DEG.count.list.e1.v3.0annotation.all %>% map(filter(FDR<0.05)) # does not work
DEG.count.list.e1.v3.0annotation.all.FDR0.05<-DEG.count.list.e1.v3.0annotation.all %>% map(function(df) filter(df,FDR<0.05)) # does work
names(DEG.count.list.e1.v3.0annotation.all.FDR0.05)
# playing with map and lapply
DEG.count.list.e1.v3.0annotation.all %>% map(~filter(.,FDR<0.05)) # does work
DEG.count.list.e1.v3.0annotation.all %>% map(nrow) # does work
map(DEG.count.list.e1.v3.0annotation.all,~filter(.x,FDR<0.05)) # does work
lapply(DEG.count.list.e1.v3.0annotation.all,function(df) filter(df,FDR<0.05)) # does work
# confirm
DEG.count.list.e1.v3.0annotation.all.FDR0.05[["root.R500.trtlive.DEGs.all.rD.v3.0anno"]] %>% View() # OK. 383 genes

```

# Reading DEGs list exp3 {data-navmenu="Reading DEGs"}
===========================================
```{r echo=TRUE, message=FALSE, warning=FALSE, paged.print=FALSE, error=TRUE}
# all model including subset data
DEG.objs.e3.v3.0annotation.all<-list.files(path=file.path("..","v3.0annotation","20180202-samples","output","FULLtoptag"),
           pattern="(^leaf|^root)(\\.)(.+)(v3.0anno)(.csv)") 
# read csv file (only full model)
DEG.count.list.e3.v3.0annotation.all<-lapply(DEG.objs.e3.v3.0annotation.all, function(x) read_csv(paste(file.path("..","v3.0annotation","20180202-samples","output","FULLtoptag"),"/",x,sep="")))
names(DEG.count.list.e3.v3.0annotation.all)<-gsub(".csv","",DEG.objs.e3.v3.0annotation.all)
DEG.count.list.e3.v3.0annotation.all[["root.cr.trtlive.DEGs.all.rD.v3.0anno"]] %>% filter(FDR<0.05)
names(DEG.count.list.e3.v3.0annotation.all)
# FDR<0.05
DEG.count.list.e3.v3.0annotation.all %>% map(filter(FDR<0.05)) # does not work
DEG.count.list.e3.v3.0annotation.all.FDR0.05<-DEG.count.list.e3.v3.0annotation.all %>% map(function(df) filter(df,FDR<0.05)) # does work
names(DEG.count.list.e3.v3.0annotation.all.FDR0.05)
# alternative way
DEG.count.list.e3.v3.0annotation.all %>% map(~filter(.,FDR<0.05)) # does work
map(DEG.count.list.e3.v3.0annotation.all,~filter(.x,FDR<0.05)) # does work
lapply(DEG.count.list.e3.v3.0annotation.all,function(df) filter(df,FDR<0.05)) # does work

DEG.count.list.e3.v3.0annotation.all.FDR0.05[["root.cr.trtlive.DEGs.all.rD.v3.0anno"]] %>% View() # OK. 3887 genes
```

# Expression pattern in exp1 {data-navmenu="Soil responsive genes in root and FPsc in exp1"}
===========================================
```{r fig.height=18, echo=FALSE, message=FALSE, warning=FALSE, error=TRUE}
# exp1 v3.0anno, root, FPsc (subset), soil responsive DEGs
gene.of.interest<-DEG.count.list.e1.v3.0annotation.all.FDR0.05[["root.FPsc.trtlive.DEGs.all.rD.v3.0anno"]] %>% filter(FDR<0.05) %>% dplyr::select(genes) %>% as_vector()
# drawing expression pattern in exp1 (using count data)
# expression.pattern.Br.graph.exp1(data=counts.exp1.v3.0,target.genes=gene.of.interest,title="exp1 v3.0",geno="both")
## using normalized expression data (cpm)
expression.pattern.Br.graph.exp1(data=left_join(cpm.exp1.root.v3.0,cpm.exp1.leaf.v3.0,by="transcript_ID") %>% rename(target_id=transcript_ID) ,target.genes=gene.of.interest,title="exp1 v3.0",geno="both")
```

# Expression pattern in exp3 {data-navmenu="Soil responsive genes in root and FPsc in exp1"}
===========================================
```{r fig.height=18, echo=FALSE, message=FALSE, warning=FALSE, error=TRUE}
expression.pattern.Br.graph.exp3(data=left_join(cpm.exp3.root.v3.0,cpm.exp3.leaf.v3.0,by="transcript_ID") %>% rename(target_id=transcript_ID) ,target.genes=gene.of.interest,title="exp3 v3.0")
```

# VennDiagram between exp1 FPsc root soil, exp3 cr root soil, exp3 un root soil. {data-navmenu="Soil responsive genes in FPsc root, exp1 and 3"}
===========================================
```{r echo=FALSE, message=FALSE, warning=FALSE, error=TRUE}
# Using annotation file for all gene list
Br.v3.0.At.BLAST <- read_csv(file.path("..","Annotation","output","v3.0annotation","Brapa_v3.0_annotated.csv")) 
# This annotation is redundant with name (Br grene). Eg 
# Br.v3.0.At.BLAST %>% filter(name=="BraA01g040570.3C")
# reduce the redundancy (112418)
Br.v3.0anno.At.BLAST.highscore <- Br.v3.0.At.BLAST %>% group_by(name) %>% arrange(desc(score)) %>% slice(1) # missing Br genes? (031319)
# length(unique(Br.v3.0.At.BLAST$name))==length(unique(Br.v3.0anno.At.BLAST.highscore$name)) # no genes missing

# DEGs of interest
e1.root.FPsc.trtlive.DEGs<-DEG.count.list.e1.v3.0annotation.all.FDR0.05[["root.FPsc.trtlive.DEGs.all.rD.v3.0anno"]] %>% filter(FDR<0.05) %>% dplyr::select(genes) %>% mutate(e1.root.FPsc=1) # 9 genes
e3.root.cr.trtlive.DEGs<-DEG.count.list.e3.v3.0annotation.all.FDR0.05[["root.cr.trtlive.DEGs.all.rD.v3.0anno"]] %>% filter(FDR<0.05) %>% dplyr::select(genes) %>% mutate(e3.root.cr=1)  # 3877 genes
e3.root.un.trtlive.DEGs<-DEG.count.list.e3.v3.0annotation.all.FDR0.05[["root.un.trtlive.DEGs.all.rD.v3.0anno"]] %>% filter(FDR<0.05) %>% dplyr::select(genes) %>% mutate(e3.root.un=1) # 287 genes
# summarize
summary.DEGS<-Br.v3.0anno.At.BLAST.highscore %>% dplyr::select(name) %>% rename(genes=name) %>% left_join(e1.root.FPsc.trtlive.DEGs,by="genes") %>% left_join(e3.root.cr.trtlive.DEGs,by="genes") %>% left_join(e3.root.un.trtlive.DEGs,by="genes")
#dim(summary.DEGS)[1]==length(Br.v3.0anno.At.BLAST.highscore$name) # TRUE. OK.
summary.DEGS[is.na(summary.DEGS)]<-0
# convert into count table
vdc<-limma::vennCounts(summary.DEGS[,-1])
# plot (classical way)
limma::vennDiagram(vdc) # traditional version

```